A method for optimizing pen-based annotations on a non-pen enabled window. The method includes starting a visible non-pen-enabled window further including position indicia and size indicia; starting a transparent pen-enabled window; and associating the visible non-pen-enabled window with the transparent pen-enabled window based on the position indicia and size indicia. The method further includes aligning the transparent pen-enabled window with the visible non-pen-enabled window, and accepting user input comprising a message. If the message further includes pen indicia, the method also includes forwarding the message to the transparent pen-enabled window. Else, the method includes forwarding the message to the first application.