Here is a great free program for batch deleting empty folders. RED (Remove Empty Directories) from Jonasjohn.de searches for empty program files folders or any folders from your computer and safely deletes it, thus saves your hard drive space.
Using this program is also simple. After installation run it. Select a directory, e.g. ‘C’ for scanning and click on ‘Scan folders’ button. After scanning finishes click on ‘Delete folders’ button to delete. You can also define some custom rules for keeping and deleting folders from ‘Settings’ tab if necessary. The program will not touch registry keys or system files.
The program works perfectly on my XP machine and it become one of my favorite applications. One disadvantage of this program is there is no provision to chose whole computer for scanning and deleting empty folders. You can download (652Kb) this program from here (Required Microsoft .NET Framework 2.0).