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)
im- 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)
dis- 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.