An apparatus and a method for an improved user interface for communicating with implantable medical devices are described. An integrated digitizer display screen and a digitizer pen serve as the primary input devices to a tablet computer adapted to receive real-time and stored medical data. The pen is used to select programming options by tapping portions of the digitizer based on visual images on the display. Additionally, the pen may be used to manipulate the medical data through the use of gestures, or be used to enter free form annotations concerning the medical data. An additional aspect of the user interface is the use of a questionnaire card to input information into the tablet computer by tapping the pen on the marked answers on the questionnaire card.