Here's the method I would use, because I'm super nerd:
1 - Open the main top level folder.
2 - In the search box, type a single asterisk ( * ) which will cause all files from that point downward (in any subfolder) to show up in the search results, regardless of which folder they are in.
3 - Drag all the search result files to their new home.
You can filter by file type too. To only copy word documents, just type *.doc into the Search box.