In this paper, a stick-slip compensation for the micro-positioning is presented using the statistical rough surface contact model. As for the micro-positioning structure, PZT (lead(Pb) zirconia(Zr) Titanate(Ti)) actuator is used to drive the load for precise positioning with its high resolution incorporating with the PID (Proportional Integral Derivative) control algorithm. Since the stick-slip characteristics for the micro structures are highly nonlinear and complicated, it is necessary to incorporate more detailed stick-slip model for the applications involving the high precision motion control. Thus, the elastic-plastic static friction model is used for the stick-slip compensation considering the elastic-plastic asperity contact in the rough surfaces statistically. Mathematical model of the system for the positioning apparatus was derived from the dynamic behaviors of structural parts. Since the conventional piezoelectric actuator generates the short stroke, a bridge-type flexural hinge mechanism is introduced to amplify the linear motion range. Using the proposed smart structure, simulations under the representative positioning motion were conducted to demonstrate the micro-positioning under the stick-slip friction.