In a method for fabricating a semiconductor device, a substrate is provided including an interlayer dielectric layer and first and second hard mask patterns sequentially stacked thereon. In one form the array optical portion comprises a transparent slide having a bottom surface with first and second gratings located to direct polarized light to the TIR surface and to direct light reflected by that surface to an imager, respectively. The scanner is also disclosed for scanning microarrays, bio-chips and areas of samples not having physical separations.