Deleting empty subdirectories seems like something Windows ought to do automatically, but for some reason that function just isn't included as part of the OS. Luckily, you don't need to download a utility to do it; instead, you can create a single line batch file that will do exactly what you're looking for:
for /f "usebackq" %%d in ("dir /ad/b/s | sort /R") do rd "%%d"
Raymond Chen, the venerable Microsoft coder, explains how this works. Basically, it uses a trick to enumerate the directories in reverse order. Since you can't delete a directory that contains data (including other directories) the only way to automate deleting directories is to start at the very bottom of the tree and work your way up.
