This powershell command will remove empty directories in the working directory:
dir -Directory -Recurse | where {($_ | dir).Count -eq 0} | rmdir
The command must be run in a powershell window. Be sure to cd to the immediate parent directory containing the empty directories you want to delete (you can double-check with the pwd command).
Use this command to check what will be deleted without actually deleting stuff:
dir -Directory -Recurse | where {($_ | dir).Count -eq 0} | rmdir -WhatIf
NB: To delete directories that contained only empty directories run the command again.