The Quran is the Prophet's miracle for all times and can not be compared to common books. Although the Quran is clear, explains matters and has conveyed the meanings through simple words as delicately and beautifully as possible, but it contains some issues and describes certain realities that we are unable to understand through our physical senses we use on a everyday basis. Although the words and phrases used are simple and not ambiguous but to understand the core of it's meanings and to draw Islamic Law from it is very difficult. Understanding the apparent meanings of Quranic verses is possible for anyone who is familiar with Arabic, because (it is evident for all who understand Arabic that) it does not consist of difficult and complicated words or words that are barely used in the language. It is also comprehendible for those who spoke Arabic with different accents.
Add to the above that Allah has not used scientific terms in the Quran. Nevertheless, in order to have a true understanding of it one should be able to recognize and distinguish between the motlag(absolute) and mogayyad(conditional), the Am(general) and khas(specific), the nasekh(abrogating) and mansookh(abrogated), the Muhkam(definitive) and the Muteshabeh (metaphorical) and the zaher(apparent) and the baten(profound) verses of the Quran.
This is why we consider the Prophet and his Household to play the role of the true interpreters of the Quran. After the Prophet’s household, Islamic scholars have strived to collect the ahadith that relate to the interpretation of the Quranic verses so that the ensuing generations could benefit from them as well.
The Quran not only has an apparent meaning but it contains many inner/hidden layers of meaning that are concealed to all people that only the Prophet and his household can explain.
Therefore one can conclude that the comprehensive understanding of the Quran requires two conditions:
First: The conditions that relate to one’s knowledge, which means to be able to understand Arabic and it's delicate and detailed meanings, the history of Islam, the sha’n nuzul (the reason and time the verse was revealed in; the occasion of revelation) for different verses as well as distinguishing between the motlagh, moggayad, nasekh, mansookh, Aam and Khas verses.
Second: The inner and spiritual conditions; to be pious and righteous and to have a pure soul; and to put away bad attributes like arrogance and pride, to strive to possess spiritual virtues and enhance them.
One of the fundamentals of Islam is that the prophet of Islam was the seal of the prophets, therefore the Quran which is his book will remain as his miracle and will guide mankind until the Day of Judgment. It is because of this that sending him leaves no more excuses for anyone to say that he had no way to any guides to the truth.
On one hand the Quran which is the miracle of the Prophet of Islam has introduced itself as "Noor", "Tebyan" and "Borhan" and insists that it is easy to understand and learn from and on the other hand it calls upon it's audience to deeply think about and ponder it's verses on several occasions and has scolded those who do not. It divides its verses into Muhkam (the verses that are clear and straightforward) and the Motashabeh (those of which are allegorical and more complicated to understand the true meaning of) in other verses. Therefore, we need to see how we can bring harmony between the two categories.
The Quran is "Noor" because it was sent down from the light of the skies and earth (which is Allah). Therefore it is clear and luminous and illuminates anything that is exposed to it, and that is why it is called "Mobin" which means clear and "Tebyan" which means a clarifier and explainer of other matters. It also called "Borhan" which means strong reasoning because it takes away all doubt and causes a solid belief that's in accord with one's "Fitrah" (inner nature that Allah (swt) has created us with).
The general understanding of the Quran
The words and phrases of the Quran have different layers of meanings, and understanding the apparent meaning which is the first meaning that comes to mind when hearing its verses is possible for anyone who is familiar with Arabic, because (it is evident for all who understand Arabic that) the Quran does not consist of difficult and complicated words or uncommon ones that are barely ever used. It is also comprehendible by those who speak Arabic with different accents. Second of all, there are no scientific terms used in it, therefore understanding the apparent meaning does not require profession in any specific field.
From the time of the prophet until now the Quran has guided people to the great levels of human values and virtues. It has shown people the path of becoming spiritual through understanding the truth of this world and doing good deeds, some of which may seem unusual to the one who has been too busy satisfying and fulfilling his material and physical desires. Sometimes acting upon these teachings requires putting away one’s arrogance and pride and surrendering to the one God.
This is the struggle that is named "Jahade Akbar" (the Great Jihad) which many people have not been able to prevail in and this itself has sometimes caused them to turn away from the "Noor" and the "Tebyan" (the Quran).
The special understanding of the Quran
The fact that the Quran has no scientific terms has made it comprehendible for people throughout time, but the Quran also conveys meanings that go beyond our senses through the words used in it, and to do so it uses different patterns and methods. Sometimes it uses tamthil (metaphors), Historical facts, Allegories, Moral lessons and etc.
In other words the Quran has been sent down for the guidance of mankind, therefore it consists of all sorts of verses (the Aam, khas, mansookh, nasekh, motlagh and moghayyad verses), because to guide humankind sometimes there needs to be temporary rulings that will be replaced with permanent ones later on.
Therefore in order to understand the Quran not only does one need to know Arabic and the sciences related to Arabic like Sarf, Nahw, Ma'ani and Bayan but he must also know the "Shan e nozool" of the verses and be able to distinguish between aam and khas, motlagh and moghayyad, nasekh and mansookh, Muhkam and Muteshabeh verses.
Therefore in order to have a comprehensive understanding of the Quran we should be able to recognize the different types of verses and put them together to reach a clear and correct understanding of the verses. This is why the Quran needs to be interpreted by the Prophet and his household. After the household of the prophet Muslim scholars have strived to collect their sayings that relate to the interpretation of the verses so that the next generations can benefit from them. According to what was said above one can conclude that the true interpreters of the Quran are the verses themselves, meaning that the first step is to gather all the verses that are related to a certain issue and then as the Quran clearly states and commands us to do so, to refer to the prophet and his household to reach the profound meaning that lies behind the words and phrases.
In this regard Imam Ali says: "The Book of Allah is that through which you gain insight, you speak and you hear. Its one part speaks for the other part, and one part testifies to the other". This is the method that was used by the household of the prophet, meaning that first they would gather the verses that related to a certain matter, compare the verses with each other, then would draw a ruling from the verses and explain the ruling for the people.
The Almighty says in the Quran: "I do not need to swear by the setting of the stars which is indeed a great oath if only you knew it - -that this is an honorable Quran preserved in a hidden Book which no one can touch (understand it) it except the purified ones, because this Quran is a revelation from the Lord of the Universe."
Therefore the household of the prophet who are the most pure and pious among people of all times are the ones who can deeply understand the Quran. In other verses the Quran introduces the prophet as the true interpreter of its verses and has commanded the Muslims to follow and obey him.
The Muhkam and Muteshabeh verses
In verse 171 of Surah Al Nisa' Allah says: "It is He who has sent down to you the Book. Parts of it are definitive verses, which are the mother of the Book (by which other verses are understood), while others are metaphorical."
The Muteshabeh verses that seem to be complicated are a good way to tell apart those who are truly knowledgeable from those who want to cause corruption and do not want to accept the truth by giving false interpretations, this is why Allah goes on to say: "Then as for those in whose hearts there is perversity, they follow the part of it which is allegorical, seeking to mislead, and seeking to give it (their own) interpretation, but none knows its interpretation except Allah And those who are firmly rooted in knowledge."
The Quran is comprised of two types of verses, the verses that are straightforward and cannot be interpreted in different ways which are called the "Muhkamat", those which relate to the other worlds (like the hereafter and the unseen ), convey deep meanings and can be interpreted in different ways which are named the "Muteshabehat"
All of the verses are comprehendible for the Rasekhoon (those who are rooted in knowledge).
Another point that lies in there being Muhkam verses in the Quran is that it shows there is always a need for divine teachers and the apostles of Allah (swt) that can show people the true and correct meaning and interpretation, the same way that some material in textbooks can only be understood when explained by a teacher or tutor, resulting in a constant need for maintaining contact with the teacher at all times and being inspired by him.
The Quran is in reality the application of the Prophet’s final will to his Ummah as he said before passing away when he said: "I am leaving behind two precious things amongst you, Allah’s (swt) book and my progeny; the two will never part until they come to me next to the Kawthar".
Who are the Rooted in Knowledge?
This term has been used twice in the Quran, once in verse 7 of Surah Ale Imran, and another time in verse 162 from Surah Al Nesa'a. In Surah Al Nesa'a Allah says: "But those of them (People of the Book) that are firmly rooted in knowledge believe in what has been sent down to you, and what was sent down before you".
The word Rasekhoon means those who are rooted in knowledge and the meaning of the term covers all scholars, but there are some instances of “those rooted in knowledge” that stand out most and can be considered the best and greatest examples for such a title, therefore when this title is mentioned these examples come to mind first.
The reason why there are numerous Ahadith that explain the "Rooted in knowledge" to be the prophet and his household, is that although the title covers all scholars and learned individuals, they are the greatest examples for the title and therefore the Prophet and his Household are mentioned when interpreting this term.
Imam Baqir (as) narrates a hadith from his father Imam Sadiq (as) in which he says: "The prophet of Islam was the greatest example of 'the Rooted in Knowledge', he knew the interpretation of every divine revelation that was given to him by Allah and Allah never revealed anything to him with out granting him and his successors the knowledge required to interpret it".
There are many other Ahadith that mention the Prophet and his household as the 'Rooted in Knowledge' in hadith sources like Usul Kafi, these ahadith have been gathered in 'Tafsir Nor Thaghalain' and 'Tafsir Borhan' and as we explained before this title can cover all scholars and the reason why the ahadith mention the prophet and his family is because they are the greatest examples of the 'Rooted in knowledge', this is why we hear that Ibn Abbas once said: "I too am among the 'Rooted in Knowledge' ".
Our understanding of the Quran depends on our knowledge and therefore those who possess all knowledge understand the Quran better than any one else. This is why the on several occasions the Prophet stressed the fact that the "Itrah" (his household) and the "Quran" are "Idls" (equivalents, two things with the same position and status) meaning that in order to understand and follow the Quran we have no way but to refer to his household.
Considering what was said above we will briefly point out what the prerequisites required to reach a comprehensive understanding of the Quran are:
1- The purity of the soul and the desire to find the truth, because the more pious one becomes the closer he gets to the "Motahharoon" (the purified, meaning the infallibles) and consequently he will be able to understand the Quran better.
One should put away his ignorance and pride, instead he should be humble and refer to the true interpreter of the Quran (the Prophet and his household), because not only does ignorance and pride keep one away from Allah it also causes the blindness and the death of his heart, stops him from understanding the Quran, veils his eyes so that he can not tell truth from false.
2- The other requirements that are needed to understand the Quran:
First: Knowing Arabic and how to read and comprehend it as well as being familiar with Arabic literature and the different fields that relate to it (like Sarf, Nahv, Maani, Bayan, Badi and Arabic vocabulary).
Second: Being familiar with the history of Islam and its course throughout time, being able to distinguish between the different type of verses, like the Aam and Khas verses, the Nasekh and Mansookh verses and the Mekki and Madani verses.
Third: To seek protection and refuge to Allah from Satan, his temptation and the 'Nafse Ammare' (the evil soul in the human being that continuously invites him to bad deeds) by saying "اعوذ بالله من الشیطان الرجیم".
Fourth: To begin with the name of Allah and ask him for his unlimited beneficence and mercy.
Fifth: To gather all the verses that relate to the same subject, because some verses of the Quran interpret and explain the other, and to refer to the Ahadith that explain the meaning of the verses, because some verses have interpretations that no one but the Prophet and his household can explain and unveil.
6- To put away all of our mindsets and previous opinions about the Ahkam we are trying to draw from the Quran so that when examining the sources we do not understand the rulings the way we want to, but rather the way they are. Therefore if we find that what the Quran is saying contradicts our opinion we should put aside our personal opinion and follow the Quran, and if one does not interpret the Quran correctly he is actually following his own desires not the Quran.
7- To have a perspective that can accept the existence of the unseen, and to rely on the Muhkam verses to explain the Muteshabeh verses. Without the Muhkam verses many of the Quranic verses may result in believing that Allah has a body or is a being like the beings we see in this world.
8- Being informed of the questions and needs of one’s time and environment, alongside awareness of the developments of science while keeping in mind some of the Quranic vows that have been fulfilled, all of this in order to be able to fulfill today’s generations needs and to be able to answer their questions according to the Quran’s perspective, without any personal thoughts being imposed on it, because as Imam Sadiq (as) says: “Allah (swt) didn’t send the Quran to a specific nation (excluding all other nations) nor for a specific time (so that it isn't for other times), but the Quran is fresh and interesting in all times and for all nations.
Of course one must be wary not to mix his own thoughts and beliefs with the Quran, because the prophet of Islam has said: “Learn the Quran and recite it, and know that it will raise you and is a means of the remembrance of Allah (swt). It is both a reserve and a valuable load that you carry. So follow the Quran and don’t do something so that it follows you [by imposing your own opinions on it], because whosoever follows the Quran, it will lead him to paradise, but whosever falls ahead of the Quran and makes it follow him, it will follow him until it casts him into the hellfire!” 
9- To have the intention to read, learn and understand the Quran to come closer to Allah and gain knowledge from the Quran, not to become famous and reach a higher position in society. One should also intend to act according to the rulings and teachings he comes across in the Quran, so that he would not be among the scholars that will be punished for not practicing what they knew, in this case he will not differ from those who never even tried to learn the religion.
10- To have hope when coming across verses that relate to Paradise and Allah's mercy, to encourage himself to obey his commands more then before, and to warn himself about Allah's Punishment if he commits sins and disobeys Allah in carrying out his commands when coming across verses that mention Hell and describe it, this way his heart and soul will become pure and he can understand more of the Quran.
11- To check our acts, deeds and behavior and in other words, to evaluate ourselves with the Quran when reading verses about the Believers and the Disbelievers and the Hypocrites to see if we bear the features and virtues of the Muminin (those of the believers that not only believe in Islam but act according to Islamic teachings). If we are not such, we should try and attain them, and if one does so he will then truly be Allah's vicegerent and successor on earth.
1- Jawadi Amoli, Abdollah, Tafsire Tasnim, vol 1, Esra’, Qom, p 15-245
2- Jawadi Amoli, Abdollah, Quran in Quran, vol 1, Esra', 1378, , Qom, p 353-458
3- Motahhari, Morteza, Khatamiyya, Sadra Publications, 1378, , Tehran, p 147-186
4- Makarem Shirazi, Naser, Tafsir Nemoneh, vol 2, verse 7 Surah Ale Emran and verse 162 Surah Nesa'a
Moddather, 31 and 36; Ghalam, 52; Saba'a, 28; Forghan, 1.
 Maedah, 15; Nesa'a, 174; Taghabon, 8; Yasin, 69.
 Ghamr, 17, 22, 32 and 40; Mariam, 97; Dokhan, 58.
 Mohammad, 24; Saad, 29; Momenoon, 68.
 Noor, 35.
 Room, 30.
 It should be kept in mind that when it comes to learning of the butun or inner and profound meanings of the Quran, it is only the prophet and imams who can do so, and no one else has the right to attribute an inner meaning to the Quran on his own. All we understand by ourselves are the apparent meanings of verses, and can only speak of inner meanings if the infallibles teach us of them.
Ale Emran, 7.
 Nahjol Balaghah, Sermon 133, …
 Refer to: Tafsir Tasnim, vol 1, p 69-73
 Wagheah, 75-79
 Hashr, 7; Nesa'a, 59.
 "ُوَ الَّذِی أَنْزَلَ عَلَیْکَ الْکِتابَ مِنْهُ آیاتٌ مُحْکَماتٌ هُنَّ أُمُّ الْکِتابِ وَ أُخَرُ مُتَشابِهاتٌ" Nesa'a, 171.
 " الَّذِینَ فِی قُلُوبِهِمْ زَیْغٌ فَیَتَّبِعُونَ ما تَشابَهَ مِنْهُ ابْتِغاءَ الْفِتْنَةِ وَ ابْتِغاءَ تَأْوِیلِهِ وَ ما یَعْلَمُ تَأْوِیلَهُ إِلَّا اللَّهُ وَ الرَّاسِخُونَ فِی الْعِلْمِ فَأَمَّا" Ale Emran, 7.
 " یَقُولُونَ آمَنَّا بِهِ کُلٌّ مِنْ عِنْدِ رَبِّنا" Ale Emran, 7.
 " وَ ما یَذَّکَّرُ إِلَّا أُولُوا الْأَلْبابِ " Ale Emran, 7.
 " انى تارک فیکم الثقلین کتاب اللَّه و اهل بیتى و انهما لن یفترقا حتى یردا على الحوض" …vol2, p 100.
 " لکِنِ الرَّاسِخُونَ فِی الْعِلْمِ مِنْهُمْ وَ الْمُؤْمِنُونَ یُؤْمِنُونَ بِما أُنْزِلَ إِلَیْکَ وَ ما أُنْزِلَ مِنْ قَبْلِکَ "
 Koleini, Osoole Kafi, vol 1, p 213.
 The famous hadith of “Thaqalain”, Biharul-Anwar, vol. 33, pg. 108. See: Makarem Shirazi, Naser, Tafsir Nemouneh, vol. 2, under verse 7 of surah Ale-Imran and verse 162 of surah Nisa’.
 Bagharah, 282; Anfal, 29.
 Motaffifin, 15.
 Rum, 52-53; Naml, 80-81.
 Fosselat, 5; Esra'a, 45.
 Nahl, 98.
 Biharul-Anwar, vol 89, p 84 and 91
 Biharul-Anwar, vol 89, p 15, Tafsir Tasnim, vol 1, p 234
 Jame Ahadith Alshia'a, vol 15, p 9 cited from: Tafsir Tasnim, vol 1, p 234.