I'm pretty sure Disk Cleanup won't do that, because index.dat and desktop.ini are system files. However, you can delete those files manually; just chose the "Yes" or "Yes to all" option in the file-deletion confimation box that will pop up when you chose Delete.

BTW- those two files are generated files; that is, Windows will recreate them as/when needed.

If you try to delete this from your profile when you're logged in you won't be able to. Log in with different user that has sufficient rights to delete files on your profile -- or -- don't worry about it