Are you using the term virus to describe malware in general, or do you have something specific in mind. The exact process changes pending the indentification of the malware.

In general, best practice says on a Windows system to boot into Safe Mode (F8) and try to run your antivirus scan from there. Safe Mode disables many process that run on system start/login and may bypass executing some virus code, making it easier to remove.
You can also perform Load Point Analysis, basically checking to see where the virus is getting started from. There are the RUN keys in the registry, as well as service keys, check the Startup folder under Programs, look in Scheduled Tasks, and even check the autoexec.bat and other cmd files, as well as your Browser Helper Objects (BHO).
Look in Add/Remove Programs for various toolbars, coupon apps, etc that you do not remember installing.
Use Explorer to view your 'c:\program files\common files' and 'c:\program files' folders, and sort by date. Often you'll see a folder date that coincides with when your system started showing signs of infection.

As a Malware SME for a large portion of my career, I can tell you there is no way to provide a solution that will work for every virus in this brief space. I hope this gives you a good start.

Richard Stiennon

Chief Research Analyst, IT-Harvest

Posted on Jan. 11, 2012

Recommended by:
Lauren Buchsbaum

I must say that removing a virus infection can be very troublesome. Malwarebytes has gotten good reviews from people I know. Try that first. The only final solution is to re-image your machine. That means re-installing Windows. This is such a common problem that there is a thriving cottage industry built up to provide this service. Geek Squad at Best Buy is one such. I was so frustrated with this process that I replaced all of our machines with Macs.

Andrew Baker

Director, Service Operations, SWN Communications Inc.

Posted on Jan. 12, 2012

I concur with what Erik has stated: While the initial diagnosis will largely be the same for many classes of malware, the remedy will greatly depend on the malware that has been detected.

And the more severe (or numerous) the malware, the greater the likelihood that rebuilding the machine will be more effective than trying to "clean" the system. Really effective malware can get deep into the system where detection can be compromised or thwarted.

Definitely start with Malwarebytes, as Richard has recommended, as it is a very good tool for identifying and addressing many forms of malware. But, for extensive infections, it might only be the first step.

-ASB: http://XeeMe.com/AndrewBaker