Piezoelectric drivers are widely used in nanoscale image acquisition systems. A source of performance degradation of these drivers is hysteresis, which introduces low rate noise and causes a slow continuous drift, decreasing the quality of scanned images. In this paper a sliding mode control policy, based on an estimator of the perturbation due to hysteresis, is applied to the control of a piezostage in a three dimensional images acquisition system, in order to improve control performances and final scanning results. The presented solution has been experimentally tested and compared with the Proportional-Integrative-Derivative (PID) controllers provided with the piezoelectric acquisition system, showing a noticeable improvement both in the piezostage behavior and in the images quality.