Quote:Yusuf, 1: Alif, Lam, Ra. These are the verses of the clear Book.
Al-hijr, 1: Alif, Lam, Ra. These are the verses of the Book and a clear Qur'an.
al-haj, 16: And thus have We sent the Qur'an down as verses of clear evidence and because Allah guides whom He intends.
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....(there are a lot more like them)
Yes, but these verses don't necessarily mean that every single verse in the Quran is going to be crystal clear to you after reading them the first time. There are certain verse that require a greater analysis than others to be understood within the proper context. So, there are two category of verses in the Quran which are called "muhkam" and "muttashaabih." The muhkam verses are clear in and of themselves whereas the muttashaabih verses are those which need to be interpreted in relation to other verses in the Quran (which are the mukham verses).
There is a specific verse in the Quran about this, which says:
“It is He Who has sent down to you (O Muhammad) the Book. In it are verses that are entirely clear (mukham); they are the foundations of the Book; and others not entirely clear (muttashaabih). So as for those in whose hearts there is a deviation (from the truth) they follow that which is not entirely clear thereof, seeking confusion and chaos (Al-Fitnah) and seeking for its interpretation, but none knows its interpretation save Allaah. And those who are firmly grounded in knowledge say: 'We believe in it; the whole of it (clear and unclear verses) are from our Lord.' And none receive admonition except men of understanding." - (Surah 3:07)
The entirely clear verses are those which have been clearly explained to establish what things are permissible and what things are impermissible (halal and haraam), to state the punishments and rewards, to command or to prohibit, to inform or to give an example, to advise or to admonish, etc. Then, the Quran says that these entirely clear verses are the foundation of the Book, meaning that they are the basis of the Book that contains the pillars of the religion and what people need to know in matters of religion and their responsibilities in matters of this life and also the afterlife. These clear verses are called the "foundation of the Book" in Surah 3:07 because they are the majority of the Quran, and therefore, it is not incorrect to say that the Quran as a whole is a clear book also.
The point is that the majority of the verses in the Quran are plain and clear in their meanings. The others, however, are a little more vague. Some people will try to interpret those verses without having a sufficient knowledge of the Quran and then they will get the wrong meanings out of the verses. This can possibly lead them into misguidance or even disbelief, and then, they will try to confuse the other Muslims also and they will try to take them away from Islam.