Deep Scan Question

I've used this product for about two weeks now and think its very handy. The only issue i'm seeing or just not figuring out is how to achieve this, but when I get the files i'm looking for I receive them in the original folders that i had them in to begin with. My issue is i want to bring that folder and all its content with it but it only brings the files within that folder. So i have to re-write all the folders and one by one re-insert the files into the original folder as i had prior to the deletion of the files. thank you for your assistance