A novel metrology method is presented for rapidly and autonomously characterizing the diameter and cutting edge radius of micro end mills using two-step optical imaging and image post-processing. This method is intended to improve on manual micro end mill geometry inspection methods in both measurement speed and repeatability. The two-step approach is used for finding the tool diameter and cutting edge radius values on two-flute 305.8-µm-diameter micro end mills: First, a low magnification and image post-processing step is used to find the tool diameter and cutting edge tip locations. The cutting edge tip locations are then used to perform a second high magnification imaging and image post-processing step to characterize the cutting edge radius values. This metrology system was used to measure a set of micro end mills and resulted in comparable measurements at an 85% reduction in measurement time and better measurement value compared with manual SEM imaging results.