1. A method for aligning a CAD image and an acquired image of a microchip, wherein the CAD image has horizontally aligned elements and vertically aligned elements, the method comprising: illuminating an area of interest in the microchip with a light beam that is linearly polarized in a first direction; collecting reflected light to generate a first acquired image of the microchip; illuminating the area of interest in the microchip with a light beam that is linearly polarized in a second direction which is perpendicular to the first direction; collecting reflected light to generate a second acquired image of the microchip; aligning the first acquired image to the horizontally aligned elements in the CAD image; and, aligning the second acquired image to the vertically aligned elements in the CAD image.