To delete an atom or a bond click the Erase button on the General toolbar then click on the atom or bond, or by dragging you can select the contents of a rectangle.

To delete the contents of a rectangle click on the Erase button and by dragging select what you want to delete.

You can delete a previously selected area by clicking on the Erase button or by pressing the Delete key. Of course the Ctrl+x shortcut works, too.