This paper presents an in-process measurement method, which is capable of conducting real-time position identification and on-machine profile characterization of micro-defects in defective microstructures by using a fast tool servo with a force sensor (FS-FTS) on an ultra-precision lathe. A real-time thrust force map is captured in the process of cutting the microstructures by the FS-FTS to indicate the cutting status with respect to the cutting tool position in the coordinate system of the lathe. Based on the thrust force map, the positions of the defects are identified in real time from the locations of the abnormal variations in the map associated with the occurrences of the defects. Characterization of the defects is then conducted by employing the force-controlled cutting tool as the measuring probe to measure the sectional profiles of the defective microstructures. The identified positions and the characterized profiles of the defects are then fed back to carry out the repair fabrication of the defective microstructures with an accurate tool path. Experiments of in-process detection and repair of the micro-defects in the microstructures over the outer surface of a roll mold were carried out to confirm the feasibility of the proposed method.