I have a bachelors degree in Physics, I have been in the army for two years doing counterintelligence and I am curious how difficult would it be to make a transition to joining the FBI. I have a clearance and have had no major criminal problems.

Federal Bureau of Investigation (http://www.fbijobs.gov/)

Try here.

Also see the following:
Join the FBI - WannaWiki (http://www.wannawiki.com/index.php?title=Join_the_FBI)