Sometimes the trojan will end up in system restore so likely is you will just bring it back out after cleaning up. You usually have to turn off restore to clear it out from there BUT bear in mind you loose ALL restore points.
Try downloading a FREE checker called Superantispyware Free adition. I have used it when i had a virus norton could not find and it worked. Just do a google for it. Also try Maleware bytes. If you can try to do the scans in safe mode.Hope this helps.