There shouldn’t be any unused files. XF automatically deletes attachments which are unused (such as a post that is never completed, or a post that is deleted).
You may need to be more specific about what the files are and where they are stored.
Chris, which Cron job should be doing it? On a test install I've done a batch update to purge most of the old content but it doesn't appear to have deleted anything from the /internal_data/attachments folder. I've manually run the daily & hourly cleanup jobs and verified that the file IDs don't show in the attachments table.