This tutorial explains how you can integrate ClamAV into PureFTPd for virus scanning on a Debian Squeeze system. In the end, whenever a file gets uploaded through PureFTPd, ClamAV will check the file and delete it if it is malware.
I do not issue any guarantee that this will work for you!
1. Preliminary Note: You should have a working PureFTPd setup on your Debian Squeeze server, e.g. as shown in this tutorial: Virtual Hosting With PureFTPd And MySQL (Incl. Quota And Bandwidth Management) On Debian Squeeze .