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The design, parameter identification and robust motion tracking control of a two degree of freedom (2-DOF) flexure-based micro/nanomechanism are presented in this paper. In the presented compliant mechanism, the cross-axis coupling ratio is below 1% indicating excellent decoupling performance. Despite this, during motion tracking the cross coupling effect cannot be ignored. To enhance the accuracy of micro/nanomanipulation, a laser interferometry-based sensing and measurement system is established. Nonlinearities such as creep/drift and hysteresis are present in this system, which are compensated with closed-loop control. Open-loop tracking results for a 1-DOF trajectory, with and without cross-axis coupling compensation are also presented. Robust motion tracking control is extended to support 2-DOF motion trajectories. This controller is implemented to track the desired trajectories over one and two axes of motion. Robust motion control demonstrates high precision and accurate motion tracking of the 2-DOF flexure-based mechanism. The cross-axis coupling is treated as a known disturbance and the performance of tracking 1-DOF trajectory, with and without cross-axis coupling compensation, is presented. Circular motion trajectories with radii of 10 μm, 1 μm, and 250 nm are also tracked. The experimental results presented in this paper demonstrate effective compensation of the cross-axis coupling with high precision motion tracking. The resultant 2-DOF closed-loop position tracking error in the X and Y axes are within ±20 nm during dynamic motion, and ±8 nm in the steady state.