The fabrication of nanoporous templates from poly(styrene)-b-poly(methyl methacrylate) diblock copolymer thin films (PS-b-PMMA, volume ratio 70:30) on silicon requires precise control of interfacial energies to achieve a perpendicular orientation of the PMMA cylindrical microdomains relative to the substrate. To provide a simple, rapid, yet tunable approach for surface neutralization, we investigated the self-assembled ordering of PS-b-PMMA diblock copolymer thin films on silicon substrates modified with a partial monolayer of octadecyldimethyl chlorosilane (ODMS), i.e., a layer of ODMS with a grafting density less than the maximum possible monolayer surface coverage. We demonstrate herein the fabrication of nanoporous PS templates from annealed PS-b-PMMA diblock copolymer thin films on these partial ODMS SAMs.