Block copolymer ordering in thin films on a preferentially wetting flat substrate is studied using a polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymer, which forms PMMA cylinders in bulk. Tapping-rnode AFM and cross-sectional TEM were employed to characterize the thin film ordered structure of the PS-b-PMMA on a flat silicon surface with native oxide that is preferentially wetted by PMMA blocks. The PS-b-PMMA in thin film develops hexagonally perforated layer (HPL), which is different from its cylindrical bulk morphology. The HPL structure of PS-b-PMMA exhibits islands and holes at the surface, which persists up to the film thickness as high as 6L(0). Surface-induced reorganization of the block copolymers on PMMA-preferring flat surface may be responsible for the formation of the layerlike nonbulk structure of HPL, which has been templated from the flat surface and propagated into a multilayered HPL films.