Through The Spiritual Eyes Of The Soul
We see that sometime a person wants to learn Torah, Midrash, Talmud or any similar subject, but he finds it very difficult to understand. He might have a question, or another difficulty, and finds it impossible to find an answer. This is not without reason. It is because of some aveira that the person committed, causing his mind to become clogged, and forming a barrier between him and the Torah. Every time a person commits an aveira, he causes a blemish in his soul. Just as the body has 248 parts, so does the soul. A person sees, mainly, not through his physical eyes, but through the spiritual eyes of the soul. When a person commits an aveira, he can blind his spiritual eyes; thus since he does not see the words he is studying, he cannot understand.
It was a custom of many of the sages that when they would study and not understand, they would confess their aveiros to Hashem and would weep with heart and soul. They would seek to find the aveira that they committed and strive to rectify it. As a result their eyes would be opened and they would understand what they were learning.