If you are just trying to pull static data from filemaker use a tab delimited file or CSV, but if you want to actually pull live data from a filemaker database, use ODBC or XML.
The current version of FMP can act as an ODBC Server (plugins to do this were available for older versions). If you are running your scripts on a platform where are supported ODBC driver is available (prob'ly windows only, but I'm not sure) you can use Win32::ODBC or DBI and DBD::ODBC to make your perl script act as on ODBC client. Check your manuals or the (surprising helpful) online help. Also read the Filemaker ODBC Primer.
IIRC, Filemaker Co. was making a big deal about using XML as a data interchange format a few years ago. I believe the web companion can spew XML as well as HTML. It should be easier to extract your data from XML files rather than HTML. Check your docs and this might help, too (it's a big PDF file, save it, and then open it).
I've been out of the filemaker game for a while, and haven't played with these features. But I know they are available (once upon I time, I yearned for them). It looks like you may even be able to trigger scripts using the ODBC interface.
Though often maligned, Filemaker is a great tool for the niche it serves. It was fun to check up on it and see how they've changed in the last few years. It looks like they are moving to integrate nicely with 'real' rdms technology, yet maintaining the ease of use that lets a secretary create and manage a functional relational database.
TGI says moo
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