Silicon-containing block copolymers are considered promising materials for high resolution pattern generation through directed self-assembly. The nonpolar organo-silicon moieties result in a high Flory-Huggins interaction parameter (χ) when paired with a polar block, allowing features well below 20 nm full pitch to be generated. In addition, the incorporation of silicon provides excellent dry etch selectivity under a variety of reactive ion etching conditions. However, similar to all block copolymer systems under development, achieving sufficiently low defect density remains a critical hurdle for implementation of directed self-assembly into high volume manufacturing. This work reports our progress towards this end, using a chemo-epitaxy flow to direct the assembly of poly(4-trimethylsilylstyrene-block-4-methoxystyrene), resulting in sub-20 nm full pitch line/space patterns. This process employs 193 nm immersion lithography to define the guide structure and is run on 300 mm wafers in a fab-like environment. Our efforts in understanding the possible root cause(s) of the dominant defect modes and reducing the total defect density of the flow will be described. This study includes research on the influence of various process parameters as well as the chemical compositions of the different materials involved, and their interactions with specific defect modes.