No wonder, before purchasing the license version this query sure comes in mind but no need to worry. Absolutely FreshMac is safe to use. You don’t need to hesitate for opting the very software and FreshMac software designed specifically by experienced professionals to scan and remove only the non-critical system files without harming your Mac system in any way.
Additionally it doesn’t mess up with stored files. FreshMac does scan of your Trash files, thus you should double-check your Trash folder to be sure that you want to remove those files.