Folders are great because they hide hidden clutter or complexity.
Try sorting your current files so that you only use one level of folders. This requires you to be:
-Less eager to make more folders
-Less apt to shove something in a "misc" folder when that misc folder would get cluttered very, very quickly
It's not a steadfast rule and not everything works with it (music collections for example) but it's a fun exercise that helps reorganize and delete the unwanted.