How do you use Atomic?.
Do you use a plugnplay module or did you made your own configuration?
If you made you own configuration, you can remove clone by making a gamelist with them. (the game list tab included in AtomicManagerof Atomic can help you to remove them).
The principle : You enable a gamelist on the advanced tab , gamelist subtab of Atomic. Then you go on the "game list" tab that appear.
you transfert all your rom from the right list to the left list using ">>" button. then in category file combobox you choose "clone.ini" , then in category you chose "clones" , and you click on "remove category" button.
then you save.
On my web site, check the "simple tutorial" , it explain how to manipulate gamelist.
If you used plunplay module, let me which one , i will say you how to proceed.