May be a delayed answer!
Create a List view with files without folder view. For achieving this, go to Create new view, under folder settings select the second radio button. Once the view is created, you should be able to see only files without any folders. Now select each file and
move to archive location or configure a workflow to make the movement. Once the files are moved to archive you can delete the copies from the current view. This would ensure that the folder structure is intact but files are archived.