A novel coordinate measuring machine (CMM) with nanometer spatial resolution and larger than 10 mm scale measuring range. ► The STM-based CMM based on an ideal structural concept was developed. ► The developed system provides high measuring stability. ► The system has a nanometer scale measuring resolution. ► The variation of the measured height among 20 measurements was 4.6 nm. ► Shapes of a steel sphere and an aspheric lens mold could be obtained by the system. 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.