This paper presents a measurement system for 3D hand-drawn gesture motion. Many pen-type input devices with Inertial Measurement Units (IMU) have been developed to estimate 3D hand-drawn gesture using the measured acceleration and/or the angular velocity of the device. The crucial procedure in developing these devices is to measure and to analyze their motion or trajectory. In order to verify the trajectory estimated by an IMU-based input device, it is necessary to compare the estimated trajectory to the real trajectory. For measuring the real trajectory of the pen-type device, a PHANToMTM haptic device is utilized because it allows us to measure the 3D motion of the object in real-time. Even though the PHANToMTM measures the position of the hand gesture well, poor initialization may produce a large amount of error. Therefore, this paper proposes a calibration method which can minimize measurement errors.