Perhaps start with a set of blocks representing available resources. The 'top' equivalent could be a stream of blocks falling down the screen. Manipulate and rearrange the blocks to create new sets of blocks representing your desired function.

Deleting a file would be similar to any current GUI file manager, but with more blocks - drag file block to delete block. Opening a file with a particular program would be similar. Chaining a series of operations would be where it gets interesting. The shape of the pieces would control what can be chained together.