Using the Erase button:
Set Erase mode on by clicking the Erase button.
To erase a single atom or bond, click on it. Deletion of the terminal bond deletes the terminal atom by default. Pressing the Alt button while deleting the bond, the terminal atom is not deleted. To change the default behavior, go to Edit > Preferences > Bonds tab and choose the desired Terminal Bond Deletion Method.
To erase a rectangular region, click at one corner of the desired region and drag the mouse to the opposite corner. While the mouse button is pressed down, a red guide will be displayed to aid you.
To select a non-rectangular region , use the lasso selection function first, then press the Erase button.
Using Selection mode:
Select a portion of the structure.
Click the Cut or Erase button or use the Delete button on your keyboard.
Using pop-up menus:
Right-click on an atom or bond.
Select Delete from the pop-up menu.