If you've configured a virus scanner on the Alfresco server all files that get uploaded to Alfresco should be virus scanned by default, as Alfresco simply streams those files to disk (to sub-folders within the alf_data directory). Alfresco renames all files using a [guid].bin filename format, so if your virus scanner is not able to autodetect MIME types from file content, or only scans executables (files with a .com, .exe, .dll, .sys, etc. extension), you may find that it doesn't properly scan files uploaded to Alfresco.
It's also worth mentioning that in some rare cases virus scanners can interfere with Alfresco (not to mention relational databases), so installing a virus scanner on an Alfresco server isn't necessarily the best idea. In that case you might consider configuring the virus scanner not to scan the alf_data directory, and implementing a custom action that forks the virus scanner and removes or quarantines the file if a virus is detected.
Cheers,
Peter
