When you remove a programm the settings (like %Appdata%) or the folders in C:\Programms wont be deleted. It would be helpful, when CCleaner search this files and delete them.
Example (I hope eyerybody undarstand what I mean):
You install Programm X:
C:\Programms\X\X.exe
C:\Documents\User\Appdata\X\X.settings
C:\Documents\User\Documents\X\helloworld.x
Now you remove this Programm, but the setup can't delete everything:
C:\Programms\X\ [empty]
C:\Documents\User\Appdata\X\X.settings[useless]
C:\Documents\User\Documents\X\ [empty]
CCleaner search now the empty folders and delete them. CCleaner scan also the folders like Appdata and search the Programm, that belong to this folder. If the programm do not exist, CCleaner delete it.
CCleaner probably will not ever have this ability as many programs require folders - even if they're empty sometimes - in order to function.
Please search the forum for "empty folders" this has been discussed. However your question is a little different, the problem is ccleaner really doesn't have a mechinism to tell 1) if an empty folder is needed, nor to tell 2) if an empty folder belongs to an installed or uninstalled program. I'm not sure how it would gain the logic to be able to pull this one off.
However, the developers do read all suggestions (though rarley comment) and they are MUCHsmarter than I.