The morphology of a thin film was studied for a binary mixture of asymmetric PS-b-PMMA block coplymers on a flat silicon wafer coated with 50 nm thick silicon oxide. AFM and TEM reveal that the PMMA cylinders orient perpendicular to the substrate by tuning thr film thickness. Futhermost, grating substrate with different width and depth are used to guide the alignment of the perpendicular cylinders. As a result, an array of highly ordered, hexagonally pasked PMMA cylinders in the PS matrix with a domain spacing of less than 25 nm has been produced.