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This paper proposes an improved sliding mode control with perturbation estimation (SMCPE) featuring a PID-type sliding surface and adaptive gains for the motion tracking control of a micromanipulator system with piezoelectric actuation. One advantage of the proposed controller lies in that its implementation only requires the online estimation of perturbation and control gains without acquiring the knowledge of bounds on system uncertainties. The dynamic model of the system with Bouc-Wen hysteresis is established and identified through particle swarm optimization (PSO) approach, and the controller is designed based on Lyapunov stability analysis. A high-gain observer is adopted to estimate the full state from the only measurable position information. Experimental results demonstrate that the performance of proposed controller is superior to that of conventional SMCPE in both set-point regulation and motion tracking control. Moreover, a submicron accuracy tracking and contouring is achieved by the micromanipulator with dominant hysteresis compensated for a low magnitude level, which validates the feasibility of the proposed controller in the field of micro/nano scale manipulation as well.