Files moved out of folders during update

When I updated the OS from 10.6.8 to 10.10.4, it moved some of my files that were in folders inside Documents and took the files out of their folders and moved them over to All My Files in 10.10.4. Is there an easy way to move large amounts of files that are in All My Files into folders? What I want to do is put the files back into folders like I had during 10.6.8 and then move those folders into Documents so that I can find them quickly. Thank you.

 

"All My Files" is a virtual folder that provides an alternate view of your files. I went to "Finder Preferences, Sidebar" and unchecked "All My Files". The existing structure was not affected.

DS