This paper describes the development of on-the-machine measuring(OMM) system which can directly measure the two and three dimensional machined accuracy using a scanning probe in milling machine. Two algorithms, NC program based continuous path(CP) measurement and CAD data assisted point to point(PTP) measurement, are developed for three dimensional measurements, with consideration of the characteristics of the scanning probe. The algorithms are used to develop an auto measuring system. The delveloped system is compared with the CMM (Coordinate Measuring Machine) in terms of accuracy and repeatability. The OMM system is expected to realize measurement time reduction and hence result in high productivity.