Versatile control of cylindrical nanostructures formed by supramolecular assembly of end-functionalized polymer blends is demonstrated not only in their orientation over large areas but also in their surface chemical functionalities. Two binary blends consisting of supramolecular analogues of diblock copolymers with complementary end-sulfonated and aminated groups are investigated, viz., mono-end-functionalized polymers of (i) one-end-sulfonated polystyrene (SPS) and one-end-aminated poly(butadiene) (APBD) and (ii) one end-aminated polystyrene (APS) and one end-sulfonated poly(butadiene) (SPBD). The orientation of the cylinders with respect to the substrate surface depends on the solvent annealing time; either hexagonally ordered vertical cylinders or in-plane ones are readily obtained by controlling the solvent annealing time. Selective chemical etching of one of the polymers provides four different chemically modified nanostructures, viz., hexagonally ordered cylindrical holes and cylindrical posts with either sulfonate or amine surface functional groups. Additional supramolecular assembly is successfully achieved by solution coating either polymers or organic dyes that complementarily interact with the functional groups on the nanostructures. Furthermore, the supramolecularly assembled nanostructures are controlled by confining them to topographically pre-patterned Si substrates with pattern geometries of various shapes and sizes to produce globally ordered vertical or in-plane cylinders with chemical functionalities on their surfaces.