I would go for a linux AV not a windows one, such as http://www.clamav.net/
they can scan windows shares and linux ones.
a windows AV (assuming it can even read a linux filesystem?) will be looking for windows system files/types and known windows virus', useless in Linux and probably won't work too well under wine either.
if wine is installed you can run windows binary executables (.exe) with wine <file>.