The 3D nano-machining and measuring system that can control with nanometer-scale accuracy have been developed in this research. In this system, the functions of position control and NC have been expanded based on surface observation function of friction force microscope (FFM). Precision positioning of cantilever was possible by using the displacement sensor in this system. Newly machining cantilever' with high stiffness was developed, and spinous single diamond grain was bonded on the end of this cantilever. Cantilevers for machining and measuring were able to exchange alternately. By using this system, 3D nano-machining and measuring was achieved.