For a scan-only, the Clamwin Kerry56 mentioned will do the scan. I would suggest running Clamwin from a bootable CD with the latest definitions rather than directly with Windows 2003 running, otherwise if the virus is active in RAM, it will continue to infect the system as the virus checker clears it.
Another option for a temporary installation is to get a trial version. Most trial versions run for 30 days and many will run on a server OS, including AVG network edition.
For USB pen drives, I would strongly recommend only using a USB pen drive if you absolutely have to on the server and if so, always scan them with a clean PC before plugging in the server. If possible, use a shared network drive to copy data to/from the server.