I did this with my Runtime long ago, as you can see in the attached image. These are mostly what I call "main folders," most of which contain many sub-folders. "Clothing," for example, is divided mostly into male and female sections, with appropriate subdivisions for armor, ordinary clothes and the ever-popular "slutware," which -- in truth -- doesn't see much use in my renders . . .  ;)

The only trouble I have now is that I've collected a lot of content over the years that I no longer use. Some of the older stuff is not high quality, but removing it involves chasing down where all the geometry and texture files have been hidden.

Sometimes, it's best to leave the old stuff in place . . .