The long-range ordering and directed self assembly of thin films of a high interaction parameter rod-coil liquid crystalline block copolymer (LC BCP), poly(dimethylsiloxane)-b-poly{2,5-bis[(4-methoxyphenyl)-oxycarbonyl]styrenel} (PDMS-b-PMPCS, or DM), is described. The LC BCP was spin-coated on a polystyrene brush functionalized substrate and then thermally annealed at different temperatures with respect to the LC ordering temperature. The effects of the wetting behavior, commensurability between the film thickness and the periodicity, and the LC orientation on the ordering and orientation of the microdomains are described. A monolayer of in-plane cylinders with excellent long-range ordering was produced, and was transferred into SiOx patterns with tunable sub-10 nm feature sizes. Well-ordered multilayer in-plane cylinders were produced in thicker films, and the correlation between microstructure evolution and the LC ordering process was studied by grazing-incidence small-angle X-ray scattering (GISAXS) and wide-angle X-ray scattering (GIWAXS). Finally, the cylindrical rod-coil BCP was directed into a novel ladder morphology within lithographically patterned substrate trenches, as well as into patterns of parallel or transverse cylinders. The ordering of cylinders, the ladder morphology, and the etch selectivity and thermal stability of this high-interaction parameter silicon-containing LC rod-coil BCP demonstrate its applicability to nanoscale lithography.