A calibration wafer and a method for calibrating an interferometer system are disclosed. The calibration method includes: determining locations of the holes defined in the calibration wafer based on two opposite intensity frame; comparing the locations of the holes against the locations measured utilizing an external measurement device; adjusting a first optical magnification or a second optical magnification at least partially based on the comparison result; defining a distortion map for each of the first and second intensity frames based on the comparison of the locations of the holes; generating an extended distortion map for each of the first and second intensity frames by map fitting the distortion map; and utilizing the extended distortion map for each of the first and second intensity frames to reduce at least one of: a registration error or an optical distortion in a subsequent measurement process.