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This paper presents the mechanical design methodologies of a 3-DOF flexure-based mechanism. A 3-RRR parallel mechanism is utilized to implement planar motions which are general requirements for micro/nano manipulation. Flexure hinges are used as the revolute joints to provide smooth motion in the range of micrometer. Three high performance piezoelectric actuators are utilized to drive the active links of the flexure-based mechanism. Finite element analysis is employed to validate the performance of the proposed 3-DOF flexure-based parallel mechanism. A novel empirical displacement mapping model is established based on the finite element analysis. This kinematic model can provide more accurate position prediction than the theoretical model where the offsets of the flexure hinges are not taken into consideration. The interaction between the actuators and the flexure-based mechanism is extensively investigated based on the established model. Experiments are carried out to verify the dynamic performance of the 3-DOF flexure-based mechanism.