A single PZT (piezoelectric) tube is generally used in atomic force microscope (AFM) as its scanner. But due to the kinematic coupling of the single tube during its bending motion, there usually exist two kinds of structure errors: vertical cross coupling error and scanning size error which affect the precision of nano observation and manipulation. In this paper, a new AFM with nano positioning stage as its scanner is developed. The stage has three PZT actuators and can move in three directions with high precision without kinematic coupling, thus the two structure errors are eliminated effectively in the new AFM. Some development results are presented and the experimental results validate the performance of the AFM.