This paper presents a high precision AFM for nanometrology of large area micro-structured surfaces. A PZT with a stroke of 100 microns is used as the Z-directional actuator for the AFM cantilever. Two capacitance-type displacement probes are aligned at two sides of the PZT along the movement direction. The displacement as well as the tilt motion of the PZT can be accurately measured and compensated for based on the probe outputs. It was confirmed that the tilt motion of the PZT was approximately 32 arcseconds over the 100 micron stroke. The sample is moved by two linear stages for scanning in the X- and Y-directions over an area of 50 mm x 40 mm. The angular error motions of the stages that influence the AFM accuracy are measured by an autocollimator for compensation. A piezo-resistive cantilever, which can output the atomic force signal by itself, was employed instead of the conventional optical force sensing device for compactness of the AFM structure. A large area sinusoidal metrology surface has been successfully measured by the developed high-precision AFM.