In this investigation, we describe a metrological technique for surface and thickness profiles of a silicon (Si) wafer by using a 6 degree of freedom (DOF) stitching method. Low coherence scanning interferometry employing near infrared light, partially transparent to a Si wafer, is adopted to simultaneously measure the surface and thickness profiles of the wafer. For the large field of view, a stitching method of the sub-aperture measurement is added to the measurement system; also, 6 DOF parameters, including the lateral positioning errors and the rotational error, are considered. In the experiment, surface profiles of a double-sided polished wafer with a 100 mm diameter were measured with the sub-aperture of an 18 mm diameter at 10x10 locations and the surface profiles of both sides were stitched with the sub-aperture maps. As a result, the nominal thickness of the wafer was 483.2 μm and the calculated PV values of both surfaces were 16.57 μm and 17.12μm, respectively.