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This paper examines the problem of time-optimal motion control in the context of scanning tunneling microscopy (STM) application and hysteresis compensation inherent to PZT actuators. The problem was divided into velocity tracking problem and point-to-point motion problem, and the time-optimal input profile was obtained using the command shaping technique of constrained least-square optimization. The optimal scanning velocity given a specific scanning distance and the effect of sampling rate has also been studied. To further improve the tracking performance, the piezoelectric hysteresis nonlinearity was modeled using the classical Preisach model, and explicitly compensated using the proposed continuous numerical inversion algorithm.