I don't know of any Perl modules which operate on Filemaker Pro files. I'm sure you're already thinking this, so I'll confirm your suspicions: It would make a lot more sense for your client to export the data into a more generically useful format such as tab- or comma-separated ASCII text files. Once you have TSV/CSV files there are plenty of CPAN modules which can do various things with them, or you can roll your own. I don't think it is very difficult to generate TSV/CSV from Filemaker.

ObPossiblyUsefulLink: Filemaker World