Folders and files in Application Data are hidden by default to protect the user from ill-advised meddling.
If you are sure that there are folders there which you thought you had removed, it might cause problems if you simply delete them as they stand.
First use the Add/remove programs in control panel to make sure they have been removed (they won't show).
Next, run CCleaner and see what that does.
If you still find stray ones there, they are probably quite small size and causing no harm.
Now you can simply delete them if you must, but it would be wise to have a full system backup first!