We employed two modes of atomic force microscopy to characterize the nanophase-separated structure of a block copolymer thin film from poly(2-methacryloyloxyethyl phosphorylcholine) and poly(3-(methacryloyloxy) propyl-tris(trimethyl-silyloxy) silane) in aqueous solution. The force-spectroscopic mapping mode clearly revealed a mismatch between nanophase arrangement and topography. This mode resolved the nanophase arrangement better than the amplitude-modulated scanning mode, whose phase-delay images were more common in visualizing the chemical distribution. Nevertheless, characterization with both modes allowed us to deduce the threedimensional structure of the copolymeric films.