There are two in- prefixes used in English. Unlike the more common un- prefix, these two are of Latin/French origin. The first in- prefix means not and comes in several forms: in-, im-, il-, ir- (by changing the N to match the following consonant). Examples include: indirect, impossible, illogical and irregular, meaning not direct, not possible, not logical and not regular.
Also this prefix rarely appears spelt en- as in enemy. Sometimes the not form of the word survives in English and its original word does not. The word enemy comes from the Latin in- (meaning not) + amicus (meaning friend).
The second in- prefix means in, as well as the related meanings to enter in, into, on or go on. As with the first in- prefix, it also comes in the forms in- im-, il-, ir- and occasionally en- . Examples include: incorporate, import, illuminate and irradiate. [These mean to include a part into a whole (have a business become a corporation), bring goods into a country, shine light on a thing, expose a thing to radiation.] Also this prefix rarely appears spelt en- as in enlighten. (Meaning to metaphorically bring a person into the light of knowledge.)
The two in- prefixes can be confused. The word inflammable means that a thing can be on fire and uses the second in- prefix, not the first. (The 3 most dangerous words in English) Another risky word is invaluable which uses the second in- prefix. For example, "Members of the public will have the rare opportunity to take a closer look at national-treasure-grade terracotta warriors and other invaluable relics from the Qin dynasty in this not-to-be-missed exhibition" (HK government press release June 13, 2012). The word invaluable does not mean not-valuable, but that it is so valuable, that no price or value can be put on it. (Meaning that it is priceless, not worthless.) To inculpate a person is to accuse them of a crime, but if they are inculpable it means that they are not culpable, or free from blame. There is some confusion between these two prefixes.
There are many words that use in- instead of un- to show the negative. They are typically words of French/Latin origin. The use of the in- prefix meaning not can be confused with the second different, but identical prefix in- meaning in. Knowing that these are the patterns should help you learning and understanding words with these prefixes.