Rootkits bury themselves deep within Windows. They intercept and alter the information that Windows provides other programs. Most security programs rely on Windows to list files on the hard drive. Rootkits remove all references to themselves and their protected files.
Fortunately, security software has caught up with hackers' methods. A handful of scans can detect rootkits.
Most of these scans work by comparing the results of two passes of the hard drive. One pass includes file information according to Windows. The other includes the results of a direct reading of the hard drive. Discrepancies indicate a rootkit at work silently making a liar of Windows.
RootkitRevealer is a free anti-rootkit scan developed by Microsoft Sysinternals. It's part of the Sysinternals Suite, which I've mentioned in the past. RootkitRevealer will list rootkit-hidden files, but it won't remove them.