There is a virus that sits in the atapi.sys file (inside C:\Windows\System32\drivers), and no other tools but this can remove it, I know because I have just removed it from my girlfriends pc and used hours to search on forums and search with online scanners, just make a search for either atapi.sys virus or virus in windows temp folder.
This virus kept making new svchost.exe files in different named folders inside windows/temp, then the antivirus made a popup, I put it in quarantine, and then two minutes after it made a new folder and the popup came again and so on.
I read somewhere that I had to put the harddrive on another pc and from there delete the atapi.sys file, but before I did that I searched some other forums and there I found some that had repaired it with Hitman35, which then removed mine to.
And as the OP also said, it's only to remove virus/rootkits/adware/spyware etc. and not to use instead of the anti virus program you have installed, it can find and remove things that many others don't.