Use Spybot Search and Destroy. I used it when I had a trojan virus and it got rid of it. It also can repair your registry if needed. What anti-virus software are you using? The one I use (Microsoft Security Essentials) detects stuff like trojans.
Here's the link to the website for Spybot and the Microsoft Security software (If you need it):
http://www.microsoft.com/en-us/security_essentials/default.aspx
http://www.safer-networking.org/en/download/index.html