Not quite sure I understand. First who allowed the user to Register? Or is it an automatic Register?
By Folders and Files do you mean jDownloads Categories and Downloads?
If so you can always change the permissions on the top level categories to a different User Group that is able to Download, and take it away from Registered UG by setting Download permission to Inherited. You would need to have a user sendable email form or similar to add them to the relevant UG