You can delete an entry (either certificate, key pair or secret key) contained in a KeyStore. There are more ways to do the deleting action:
Edit Menu > Delete
using the context menu (by clicking the right mouse button and
using the Delete toolbar icon;
use the keyboard shortcut, by default
Note that a "Confirm Entry Delete" window will be displayed first, so the user has the possibility to change his mind regarding the delete action. In case of the native Windows Root KeyStore the OS will prompt for a native confirmation dialog as well.