In the end, I came up with an architectural-styled paper sculpture where the base rectangular area is the root folder and the other stacks of rectangles are the subfolders within that root. The height of each folder is denoted by the number of files that it contains. I decided only to visualize 3 levels deep, otherwise it would become too complex.

And here are my concepts

One problem I realized halfway through construction was that I had cut the sizes of the subfolder rectangles to fill up the entire root folder rectangle – this actually made it quite difficult to distinguish the actual boundaries of each subfolder. Higher up in the structure, however, I allowed for more room between the stacks, which makes it easier to understand. In 3 weeks I will be exhibiting my work with my classmates, so I will have these problems resolved by then.