Are There Any Rules For Using Prefixes?

Yes, there are, although some things about prefixes are quite arbitrary. Unfortunately the commonest prefixes of all, un- and in- , are interchangeable and just have to be learnt.
Otherwise, there are some helpful rules, mainly about negative prefixes:
Ir- appears only before words beginning with "r" (regular, relevant)
il- is before "l" (legal, legitimate)
I'm- is before "m" or "p" (immeasurable, impossible)
A note of caution, though; while the above prefixes can only be used with the letters shown, the letters themselves are often used with other prefixes (unreliable, unlawful, unpatriotic)
mis- always has the sense of a mistake being made (misunderstand, misfire)
this- has the sense of change or difference rather than absence/lack, e.g. "dissatisfied" means that you're not happy with the quality of something that you've got, whereas "unsatisfied" suggests a lack of something. (If you're dissatisfied with your restaurant meal you complain; if unsatisfied, you order more.)
With most other prefixes, it's not so much a question of rules as of learning their meanings: Pre- means before, post- after, and so on.

I don't completely agree with Paulaw. There are some other "le" words that do not take the "il" prefix (mislead, unleash).
Also, there are other words with "il" prefixes that do not have "le" (illogical, illiterate).
"dislike" is an exception for the "l+another vowel" rule after the prefix "un."

I hate exceptions...so frustrating for my ESL students!  I just tell them to memorize and read as much as possible...