Cylinder-forming polystyrene-block-poly(methyl methacrylate) (PS-b-PMMA) thin films were directed to assemble on chemically nanopatterned surfaces consisting of a square array of spots with varying diameters of lattice spacing and spot size. In all cases the patterned spots were preferentially wet by the PMMA block in a continuum of surface wet by the PS block. On this chemical pattern, cylindrical domains oriented perpendicular to the surfaces formed a square array of vertical cylinders, instead of a hexagonal array typically formed in the bulk morphology of cylinder-forming block copolymers. When the lattice spacing of chemical spot patterns was incommensurate with the natural dimension of diblock copolymer in a square array, surface reconstruction led to the formation of microdomain structures that do not appear naturally in the bulk state, such as a loop structure of PMMA cylinders connecting two neighboring PMMA cylindrical sections, and semicylinder domains located at the center of the square unit cell, which did not contact the bottom substrate. The chemically nanopatterned surface became ineffective at forming vertical cylinders with a square array when the cylindrical domains were a distance of 1.5 times the bulk cylinder diameter from the patterned surface. The novel morphologies and the variation of morphology with film thickness shed light on the reconstruction of the microphase-separated block copolymer morphology as it equilibrates in the presence of a chemically nanopatterned substrate.