Well first Id disconnect it from the internet then depending on what tools you have you could plug the HDD in as a slave and run a scan on it removing the infections making sure to log the actions so that you can tell what was there and what has happened or if your not able to slave the HDD you can run a live CD to scan for infections. After infections are removed I would then try and clean up what the infections did, lets say if they added user accounts or registry entries, Id run programs made specifically for said infection or just ccleaner to clean up the registry. There are popular programs like HiJackThis that you can run also.
If I get trojan or owt I go down the radical route. I format and install new system. I dont find it pain to do new install and I often sling in new system just becuse I am bored... Usually quite carefull and try not to let owt in to begin with,just wish the rest of the familly did the same.
Well in my work i usually reboot in safe mode with network support then i use malwarebytes complete scan then i use superantispyware cuz often it founds such things that malware hasn't seen and finally i go through system with avast home version cuz i never use cracked antivirus and usually these steps help me but i always update these softs to latest virus base but if you have specific virus like fake antivirus then i use remove fake antivirus. So good luck in virus catching