This paper examines a new in-process measurement system for the measurement of micro-defects on the surfaces of brittle materials by using the AFM (Atomic Force Microscopy). A new AFM scanning stage that can also perform nano-scale bending of the sample was developed by adding a bending unit to a commercially available AFM scanner. The bending unit consists of a PZT actuator and sample holder, and can perform static and cyclic three-point bending. The true bending displacement of the bending unit is approximately 1.8mm when 80 volts are applied to the PZT actuator. The frequency response of the bending unit and the stress on the sample were also analyzed, both theoretically and experimentally. Potential surface defects of the sample were successfully detected by this measurement system. It was confirmed that the number of micro-defects on a scratched surface increases when the surface is subjected to a cyclic bending load.