Is it possible to replace/prepend the file name on upload with some member data?
For example original file is called file_data.zip but then prepend the filename with third_hyperion_991 leaving third_hyperion_991_file_data.zip
http://php.net/manual/en/function.rename.php
Suggestion: Use the file_after_save
hook to simply rename the file in a custom extension. You will then have to update the related file info in the database (and probably where it's connections live in your channel data rows).
This assumes you are using a native file field in FreeForm. If you're using an assets field, the hook might be different. If using assets, one of these suckers will be your prize:
http://docs.pixelandtonic.com/assets/developers/hooks/index.html