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This paper focuses on the open-loop and closed-loop position control of a three degree-of-freedom (DOF) compliant micro-motion stage with flexure hinges. This micro-motion stage has a parallel structure for better stiffness and accuracy than serial structures and is driven by three PZT stack actuators. It was discussed in the authors' previous paper that due to the limitation of current modeling methods for compliant mechanisms the derived kinematic model is not able to accurately describe the behavior of the investigated micro-motion stage. Therefore, an experimentally determined constant Jacobian matrix is used to relate the extensions of PZTs and the end-effector movement for position control. With the use of the experimentally determined Jacobian in open-loop control, the micro-motion stage is proved able to achieve good positioning accuracy. Nevertheless, the positioning accuracy is significantly improved by incorporating end-effector closed-loop control.