There are two Freeware tools (which i like most) for deleting empty folders
1. RED (Remove Empty Directory)
Type: Freeware & open source
About: RED searches and deletes empty directories recursively below a given start folder and shows the result in a well arranged tree. Further you can create some custom rules for keeping and deleting folders. Empty files in directories can also be ignored. Just try RED to see the other features - no registry keys or system files will be touched.