As industry of a semiconductor and LCD industry have been rapidly growing, precision technologies of machining such as etching and 3D measurement are required. Stylus has been important measuring method in traditional manufacturing process. However, its disadvantages are low measuring speed and damage possibility at contacting point. To overcome mentioned disadvantage, non-contacting measurement method is needed such as PMP(Phase Measuring Profilometry), WSI(white scanning interferometer) and Confocal Profilometry. Among above 3 well-known methods, WSI started to be applied to FPD(flat panel display) manufacturing process. Even though it overcomes 21t ambiguity of PMP method and can measure objects which has specular surface, the measuring speed and vibration coming from manufacturing machine are one of main issue to apply full automatic total inspection. In this study, We develop high speed WSI system and algorithm to reduce unknown noise. The developing WSI and algorithm are implemented to measure 3D surface of wafer. Experimental results revealed that the proposed system and algorithm are able to measure 3D surface profile of wafer with a good precision and high speed.