Being unfamiliar with filemaker, I don't know what it's capeable of exporting. However mySql will readily take a sql file for creating databases, tables and inserting data. However it gets tricky in what syntax filemaker uses to make it's sql exports.
There will be plenty of db converters on the open market that will do the job for you. Thing is, they're always fairly expensive. Ask Mr Google "filemaker +converter +mysql", and I'm sure he'll point you in the right direction.
