Abstract: This disclosure provides a high precision measurement system for rapid, accurate determination of height of a deposition source relative to a deposition target substrate. In one embodiment, each of two transport paths of an industrial printer mounts a camera and a high precision sensor. The cameras are used to achieve registration between split transport axes, and the positions of the high precision sensors are each precisely determined in terms of xy position. One of the high precision sensors is used to measure height of the deposition source, while another measures height of the target substrate. Relative z axis position between these sensors is identified to provide for precise z-coordinate identification of both source and target substrate. Disclosed embodiments permit dynamic, real-time, high precision height measurement to micron or submicron accuracy.