Demands for measurement of three dimensional (3D) micro-geometries over a large area have recently increased in a variety of industries. In order to meet such requirements, it is necessary to realize a novel coordinate measuring machine (CMM) with a three-dimensional nano-motion system which has high resolution, high response and large measuring area. In this study, a three-dimensional nano-motion system was developed for a scanning probe microscopy (SPM) based CMM with nanometer spatial resolution. The system developed is composed of an X-Y planar nano-motion table system driven by voice coil motors (VCMs), a Z axis nano-motion system driven by a hybrid actuator and a probe holder that equipped with SPM probes. Performance evaluation results confirm that the system simultaneously achieves a long travel range, a high positioning resolution and a high stability.