The subject invention relates to a wafer stage, such as may be used in optical wafer metrology instruments. The stage contains a wafer-chuck that can be connected to translation stages for the purpose of clamping and translating the wafer so that a plurality of sites on the wafer surface may be measured. The chuck includes a holder for mounting a reference sample. The holder is movable between a retracted position where the reference sample is held below the chuck surface and an extended position, such as where the surface of the reference sample is co-planar with the wafer surface. Therefore the holder may be installed within the area of the chuck that is utilized for wafer clamping. By this arrangement, the size of the wafer translation system can be reduced minimizing the stage travel and enabling increased spatial resolution, increased wafer throughput and reduced capital equipment and operating costs.