Windows 7 computer with the latest free Avira AV installed and it scans running processes, the registry, and all files from Safe Mode. After loading the computer into Safe Mode with a user login that has admin rights, click on the start button, then 'All Programs', then Avira, then "Antivirus", then "Start Avira Antivirus". When that opens, make sure to click on "Extras" in the upper left, choose "Configuration", then make sure the System Scanner is set to scan all files. If you make changes, click on "Apply", then OK, then click on the "View" menu in the upper left corner, choose "Status", then click on the "Scan System" button. It should now scan all files.
If it doesn't, then the computer may be infected and needs an outside intervention tool such as the AVG Rescue disc mentioned by Bob, or the Avira Rescue Disc which performs a similar scan outside of Windows upon boot of the disc.
Hope this helps.