Running host-based anti-malware software is a very good idea, but sometimes things can slip through. You can't trust an infected machine to tell you whether it's infected or not. Microsoft has System Sweeper, which boots from another media and will scan a Windows machine. There is one version for 32 bit Windows and one for 64 bit Windows.
Kaspersky Labs has a Rescue Disk that will also scan a Windows machine offline.
If malware is discovered I would recommend rebuilding the system and restoring the data. In my opinion, these tools should be used periodically to determine to some extent that a system is malware free. Of course, it is a judgment call, depending on what is found.