The bootable CD anti-virus I use is the Avira Rescue Disc...there are
others:
http://www.free-av.com/en/products/12/avira_antivir_rescue_system.html
These instructions should be read carefully before beginning:
Tutorial for Avira Rescue CD -
http://forum.avira.com/wbb/index.php?page=Thread&threadID=82163
Note there is also an Update button in the program, and if you are
connected online with a permanent broadband connection, it will be able
to update if you select it.
The configuration settings shown in the tutorial have Avira attempt to
repair infected files, and rename if not successful. This is generally
the best option, but I often run it with the 'protocol malware records
only' setting instead, so I can read the resulting log *without* having
fixed anything. That way, if a root kit has infected a critical system
file, I can determine where and how to find a clean replacement file,
and how to go about copying the good file after I do a cleaning by
re-running the Avira Rescue CD with the settings at 'repair or rename'.
Generally I will replace a file using the command line in Recovery
Console.
The Linux-based Avira CD sometimes has a problem running on some
laptops, due to driver issues.
If I slave the drive to another computer, I will run the AV from that
computer on the drive (Avira or Avast or MSE, depending on which system
I connect it to). I will also consider running the Protection Scan
online from OneCare, selecting the slave hard drive:
http://onecare.live.com/site/en-us/center/howsafe.htm
If doing all that is beyond what you feel comfortable doing, you should
find a competent computer repair technician who will follow these
procedures on your system.