Your questions are building on top of one another. Did you try using BioPerl to loop through the files in the directory, and then adding the reg-ex to it? That's 90% of the battle, and if you did you'd probably get more helpful and enthusiastic responses.

People don't mind helping, but try to show that you're learning and making an attempt. A nice way to prove that, as Abigail said, is to show either a code fragment or a list of what you've tried.