Empty folders or directories exist for a number of reasons. Sometimes applications create and require empty folders and deleting them can cause your programs not to function as they should. Usually though, empty folders are a results of sloppy uninstallation programs that fail to clean up all traces of programs. The result can be hundreds of empty folders. While these won't harm your computer, they could slow it down since at various times Windows must read into memory the folders that you have on your computer. Getting rid of unneeded ones can only help.
Most empty folder removal tools are command line only and therefore not so easy to use, but German programmer Jonas John has created a Windows based tool called Remove Empty Directories which is free for use. The program is easy to use. You select a folder or drive to scan, click Scan Folders and the program goes to work. An Options Panel lets you specify certain folders that should not be flagged as empty.