This paper aims to develop a position tracking controller for a micro-gripper's tip. The controller should be robust, able to compensate external disturbances and perform precise reference tracking under parameter variation and incertitudes. It becomes clear when considering the gripper's response on two different environments: air and vacuum. In this work, two models were identified based on experimental data, one for each case of study, and an extended high-gain observer controller based on output feedback is proposed. Simulations show that the controller, chosen to achieve a desired performance for the system in air, is able to maintain similar results in vacuum. The proposed setup was implemented in real-time for the system in air and simulated for vacuum.