Unless your algorithm is broken so much that you somehow visit each node more than once, any code improvements will be insignificant compared to the disk access time.

If you want it to be faster, try using a ram disk to build your pruned tree and then xcopy /s it to the harddrive in one go when you're done.

Not worth rewriting it in this case, but in general situations you should consider using an iterative loop instead of recursive calls.