Use one of your Windows clients to scan the files served by your Samba server. You could even install a Windows VirtualBox guest on your FreeBSD computer to perform the scan. Obviously, your scanning process should have access to your Windows clients disk space as well.
If it has to be done from the server, then the clients will have to share their drives so the server can get to them. But maybe you mean that the server just needs to receive results of the clients' own antivirus scans of their drives. That would depend on what antivirus software is being used, but there are monitoring framework things like http://www.nsclient.org/ that might work.
On a closely related note since you mention Samba, there is the security/samba-virusfilter VFS module that may fill a future need. It may be useful if you don't want to completely trust the client configuration you end up implementing.
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