A mechatronic system based on the micro-macro-kinematic consists of an industrial robot and a piezoelectric stage mounted on the robot’s end-effector and has to carry out operations like micro-assembly or micro-milling. The piezoelectric stage has to compensate the positioning error of the robot. Therefore, the position of the robot’s end-effector has to be measured with high accuracy. This paper presents a high accuracy 6D-measurement system, which is used to determine the position and orientation of the robot’s end-effector. We start with the description of the operational concept and components of the measurement system. Then we look at image processing methods, camera calibration and reconstruction methods and choose the most accurate ones. We apply the well-known pin-hole camera model to calibrate single cameras. Then we apply the epipolar geometry to describe the relationship between two cameras and calibrate them as a stereo vision system. A distortion model is also applied to enhance the accuracy of the system. The measurement results are presented in the end of the paper.