On single drive you run a variation where you read X MB of data to a buffer, then write X MB of data out, then execute deletes, and so on. This lets avoid some of the problems with small files. Not all, because small files will unlikely to be consecutive, the head will have to jump a lot, and then you still need to do a lot of small writes to filesystem (to remove the files).

There are obviously improvements you could do. For some filesystem you can just remove entire folders rather than remove the files individually just to remove parent folder.