The main driver for Semiconductor and Bio-MEMS industries is decreasing the feature size, moving from the current state-of-the-art at 22 nm towards 10 nm node. Consequently smaller defects and particles become problematic due to size and number, thus inspecting and characterizing them are very challenging. Existing industrial metrology and inspection methods cannot fulfil the requirements for these smaller features. Scanning probe Microscopy (SPM) has the distinct advantage of being able to discern the atomic structure of the substrate. It can image the 3D topography, but also a variety of material, mechanical and chemical properties. Therefore SPM has been suggested as one of the technologies that can fulfil the future requirements in terms of resolution and accuracy, while being capable of resolving 3D futures. However, the throughput of the current state-of-the-art SPMs are extremely low, as compared to the high-volume manufacturing requirements. This paper presents the development of an architecture for a fully automated high throughput SPM, which can meet the requirements of future process metrology and inspection for 450 mm wafers. The targeted specifications of the concept are 1) inspecting more than 20 sites per wafer, 2) each site with dimension of about 10 × 10 μm2 (scalable to 100 × 100 μm2) and 3) with a throughput of more than 7 wafers per hour, or 70 wafers per hour with a coarse/fine scanning approach. The progress of the high throughput SPM development is discussed and the baseline design of the critical sub-modules and the research issues are presented.