Yes. You can use a Linux Anti-virus suite. There are several. They are of
little use in Linux, so it is their chief purpose is to scan Windows files.
You can also download one of several free Linux Live CDs for this purpose.

http://www.sysresccd.org/Main_Page
trinityhome.org/Home/index.php?wpid=1&front_id=12
http://www.livecdlist.com/

There are Linux versions of several Windows AV applications such as AVG,
Avira, Bitdefender, as well as Clam or Klam.

http://free.avg.com/us-en/download.prd-afl
www.ghacks.net/.../
www.ghacks.net/.../