Virus scanners operate by searching your hard drive(s) for files which might be infected by a virus. This method is never 100% secure, since only known viruses (or known virus patterns) are detected. That is why you update your anti-virus often. If an infection has been detected in a certain file, the virus scanner might be able to clean the file, but very often this is not the case. In that case, you can try another scanner to clean the file, you can try to replace the file or - as a last resort - delete it.
However, if many important operating system files are affected, it might be the best solution to reformat the hard drive and install the operating system from scratch. Back up all files on a CD, flash or thumb drive or another external hard drive.
There are even viruses that can not be cleaned by mere hard drive reformatting. The boot-viruses infects the boot-sector of disks, and will very often not be removed by simply reformatting the hard drive. In this case you will need to repair the boot-sector. Your first line of defense is a firewall, next is an updated anti virus program. There are many anti-virus programs, they can cost you lots of $$$. I use a free antivirue program from Gibson Research Corps. I've used it for a number of years, found it very user friendly. It can be set to auto update, or you can check for updates at anytime.