The optimization of a grapho-epitaxy process flow for lamellar phase block copolymer frequency multiplication on full 300 mm wafers is discussed. The process uses a dedicated photoresist that, after hardening, allows direct coating and annealing of the block copolymer over it. Some of the critical parameters for optimization of this process were found to be the selection of the neutral layer material and reduction of the prepattern resist height. Process window analysis was done by determining the best dose and focus settings for generating high quality directed self-assembly structures with the prepattern process. A very small process window for good self-assembly and an offset in the optimum dose and focus settings for these two stages of the process were found. Finally, the sensitivity of the process to programmed prepattern imperfections was studied. Programmed protrusions in the prepattern as small as 6 nm were found to cause self-assembly defects.