Nowadays most overlay metrology tools assess the overlay performance based on marker features which are deposited next to the functional device features within each layer of the semiconductor device. However, correct overlay of the relatively coarse marker features does not directly guarantee correct overlay of the much smaller device features. This paper presents the development of a tool that allows to measure the relative distance between the marker and device features within each layer of the semiconductor device, which can be used to improve the overlay at device feature level. In order to be effective, the marker to device feature distance should be measured with sub-nanometer measurement uncertainty over several millimeters range. Furthermore, the tool should be capable of profiling the marker features to allows prediction of the location interpretation of the optical diffraction based alignment sensors, which are sensitive for potential asymmetry of the marker features. To enable this, a highly stable Atomic Force Microscope system is being developed. The probe is positioned relative to the wafer with a 6DOF controlled hexapod stage, which has a relatively large positioning range of 8x8mm. The position and orientation of this stage is measured relative to the wafer using 6 interferometers via a highly stable metrology frame. A tilted probe concept is utilized to allow profiling of the high aspect ratio marker and device features. Current activities are aimed at demonstrating the measurement capabilities of the developed AFM system.