We demonstrated a process to create nanoscopic templates for the nanofabrication of patterned media using thin films of diblock copolymers. The self-assembled monolayers (SAMs) technique is used as a means to chemically modify the topographically confined trench surfaces to manipulate the wetting behavior of cylindrical diblock copolymers and perpendicularly oriented cylindrical poly (styrene-block-methyl methacrylate) (PS-b-PMMA) copolymers are obtained. Through optimizing the annealing conditions. long-range ordering in trenches is achieved after annealing at 170 degreesC for about 24 h. The ordering is strongly dependent on the line-edge-roughness (LER) of the trenches and the number of defects in the copolymer films inside the trenches. Efforts to decrease the various defects in the copolymer films and improve the trench LER are still in progress. With our approach, a negative phase 20 nm nanoporous SiO2, template and a positive phase 20 nm Ta nanodot template based on the self-assembled cylindrical PS-b-PMMA block copolymers are feasible for following pattern transfer to make patterned media. (C) 2004 American Vacuum Society.