A system and method for operating a window of an automotive vehicle having a convertible top includes at least one powered window selectively driven by a motor. A controller is operatively connected to the motor and sends a signal for positioning the powered window to one of a raised or lowered position in response to lowering of the convertible top. An input or selector is operatively associated with the controller that allows a user to select one of the raised and lowered positions of the at least one powered window in response to lowering the convertible top. Further, a temperature sensor provides a signal indicative of the external temperature and/or a vehicle speed sensor provides a signal indicative of the vehicle speed so that positioning of the window can be temperature dependent and/or vehicle speed dependent.