The safest way to clear cookies is from all browser you have. Run your browser and find a way to go to the menu option of the browser. You can clear cookies, history, or even saved password. But if your PC is totally on your only hand then you can leave the saved password. In case you forget or don't want to be bothered by having to type a user name and password again and again.
edit: If you mean it to have more space on your Windows drive then you open the drive property (right click on drive C icon) and click disk cleanup, it offers you what files you wnt to delete.