We report a facile method to control directed self-assembly (DSA) of spherical micelles of block copolymers (BCPs) by topographically patterned surface. A cylinder-forming polystyrene-block-poly(2-vinylpyridine) copolymer [M-n,M-PS = 175 kg/mol, M-n,M-P2VP = 70 kg/mol, and polydipersity index (PDI) = 1.08] was phase-separated on a thin film of poly(vinyl alcohol) (PVA) by solvent annealing. By additional treatment with ethanol as a preferential solvent for P2VP block, the surface of BCP thin film was reconstructed to produce nanopores. Nanoporous structures in BCP thin films were transferred to the underlying hydrophilic PVA film by reactive ion etching (RIE). Then spherical BCP micelles were quickly self-assembled within the nanopores in the PVA layer due to topographical contrast and surface energy difference during spin-coating. Consequently, the site-selective array of BCP micelles was utilized as templates to achieve heterogeneous organization of nanoparticles and organic fluorescent dyes over a large area. In addition, it was observed that those heterogeneous assemblies showed a remarkable decrease in fluorescence intensity of organic dyes.