Well, the safest thing to do would be backup all important files, format the hard drive(s), reinstal windows or whatever you're using, and put a good firewall, antivirus and stuff like that on the hard drive.
(i got 4 protection systems runningn at the moment, you can never be safe enough!)
this could turn out ugly if it's a virus that set a backdoor open for the trojan. You could just be copying the virus back after the format.
