1. CWShredder - http://www.intermute.com/spysubtract/cwshredder_download.html
Just download the standalone version - http://cwshredder.net/bin/CWShredder.exe
2. TrojanHunter http://www.trojanhunter.com/
3. Ad-aware SE - http://www.majorgeeks.com/download506.html
4. Spybot-Search & Destroy - http://www.safer-networking.org/index.php?page=mirrors
5. You can also try to use Microsoft Antispyware. It is top among others as per Eric Howes test guide but is in beta though. http://www.microsoft.com/athome/security/spyware/software/default.mspx

Before running a scan:
1. Review your Add/Remove programs to see if you have unwanted or suspicious items in the list. Uninstall the unwanted items.
2. Update the the above security programs
3. Configure by following the recommended settings:
- For Ad-aware SE - see: http://www.lavasoftsupport.com/index.php?showtopic=48134
- For Spybot Search & Destroy - see: http://spybot.safer-networking.de/en/tutorial/index.html

3. Get the Ad-aware SE add-on VX2 Cleaner from http://www.lavasoftusa.com/software/plugins
Follow the instructions on how to install and use.

After the scan and if you will still see pop-ups, verify that Messenger Service is disabled. Note: Messenger Service is NOT the Windows or MSN Messenger application.
To disable Messenger Service, simply download Shoot the Messenger from http://grc.com/stm/shootthemessenger.htm

It will help know the issue if you will post the exact location that your antivirus found. Also the threat name.