A TWC forum post asking is it safe to delete empty folders, made me search for some good empty folder deleting freeware. While you would make no real space savings as they occupy 0 bytes, if it is just good house-keeping you are looking, it may be a good idea. Do read the forum post before you proceed.
Delete empty folders & directories
There are several free software available to delete empty folders. Here are four I came across:
Empty Folders Finders
Remove Empty Directories shows the empty directories before deleting them, supports multiple delete modes (including Delete to recycle bin), allows white and black listing of directories by using filter lists and can detect directories with empty files as empty. It allows you to ignore certain directories and offers various other options. It also identifies Protected folders.