A system and method is disclosed for performing matched drilling operations on mating first and second workpieces. A microscopic camera is mounted on a movable spindle holding a tool. A micro-adjustment mechanism on the spindle controllable moves the tool. A template is provided that is mounted to the first workpiece and to the second workpiece. A controller receives images of the template from the microscopic camera at each of the predetermined positions on the first workpiece and identifies microscopic features on the template associated with each of the predetermined positions on the first workpiece. The controller compares microscopic features within received images of the template at each of the predetermined positions on the second workpiece associated with microscopic features of a corresponding image of the first workpiece to calculate a necessary offset adjustment that is applied to the micro-adjustment mechanism before each operation on the second workpiece.