Demands for precision measurement of three dimensional micro-geometries over a large area have recently increased in a variety of industries. In order to meet such requirements, it is necessary to develop a novel coordinate measuring machine (CMM) which has high resolution together with larger than 10 mm scale measuring range. This paper presents a newly developed CMM with nanometer spatial resolution based on a scanning tunneling microscopy principle. The developed CMM is composed of a planar nano-motion control system driven by voice coil motors and a vertical nano-motion system driven by a hybrid actuator. Furthermore, in order to achieve long-term stability and repeatability, the machine is installed on an active vibration isolating system inside a temperature-controlled enclosure. Performance evaluation results confirm that the CMM has nanometer spatial resolution, large measuring range and high structural stability.