Given a list of files (generated via File::Find or something), you could try opening each one with Audio::WMA and see if you can read any info from them. If you can, then do something with it, otherwise leave it alone. I'm almost sure this wouldn't be failsafe. In fact, it might be more accurate to do it the other way, trying to detect if the file is an MP3 (see the many MP3 modules) and then separate them.

Update Using File::MimeInfo might be the best solution in determining the filetype.