A method for determining a surface quality of a substrate sample using a differential interference contrast microscope is described. The microscope includes an eyepiece, an eyepiece focus adjustment, a microscope focus adjustment, a light source, at least one of an aperture or reticule, a camera view, a prism and an eyepiece. The method includes calibrating the focus of the eyepiece with the focus of the camera and determining a peak response ratio for the microscope through adjustment of phase between differential beams of the microscope. The substrate sample is placed under the microscope, illuminated with the light source, and brought into focus with the microscope focus. Phase between differential beams is adjusted, at least one image of the substrate sample is captured and processed to determine a level of surface structure on the substrate sample.