I've had some experience with trojans.  My nephew is an online gamer and totally dumb when it comes to accepting things from gaming sites that he should not accept. :D 
We have  cleaned his computer of everything from trojans to key loggers.

After you get it cleaned..go to an online site like McAffey or Grissoft and run a virus check on your computer from there...just in case the trojan disabled any part of your security on your home machine.
The only program files I've had infected would be java files and you can purge your java cache from your machine. But before you transfer files..i would definately go online and do a virus check..AND remember to keep your antivirus turned on when you do go online. :D   If you need to turn it  off the antivirus website will walk you thru it.

Good luck

 

“For those who believe, no proof is necessary. For those who don't believe, no proof is possible.”

[Stuart Chase]