The surface structure of the polyimide alignment layer has been probed by various tools, but a direct visualization of the treated layer surface over a sizable area is lacking. We demonstrate Brewster angle microscope imaging of the micro-grooves formed on a rubbed polyimide alignment layer, compared with the flat surface image of a photo-aligned polyimide surface. Textures of cholesteric liquid crystal on these alignment layers showed that the rubbing causes a nonuniform orientational alignment of liquid crystals, in contrast to a uniform orientation in the photo-aligned cell. This tool enables early detection of surface defects in alignment layers, which would significantly reduce the failure in liquid crystal display fabrication.