It's very difficvult to get rid of the trojan file that's running. Since you know the file concerend, you could put the drive onto another PC (e.g. via a USB enclosure) and remove it (and any others created around the same time) there. Reboot in safe mode in the original PC, rerun PYBOT or whatever; then a registry cleaner. If you got all the files in the delete operation and if windows wasn't damaged by the trojan, you should be OK.