You Can't Trust an Infected Systems Virus Scan
https://connect.microsoft.com/systemsweeper
Kaspersky Labs has a Rescue Disk that will also scan a Windows machine offline.
https://support.kaspersky.com/faq/?qid=208282173
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.