Block copolymer (BCP) microphase separation at substrate surfaces might enable the generation of substrate features in a scalable, bottom-up fashion, provided that the pattern structure, orientation, and alignment can be strictly controlled. The PS-b-PDMS (polystyrene-b-polydimethylsiloxane) system is attractive because it can form small features and the two blocks can be readily differentiated during pattern transfer. However, PS-b-PDMS offers a considerable challenge, because of the chemical differences in the blocks, which leads to poor surface wetting, poor pattern orientation control, and structural instabilities. These challenges are considerably greater when line patterns must be created, and this is the focus of the current work. Here, we report controlled pattern formation in cylinder-forming PS-b-PDMS by anchoring different types of hydroxyl-terminated homopolymer and random copolymer brushes on planar and topographically patterned silicon substrates for the fabrication of nanoscale templates. It is demonstrated that non-PDMS-OH-containing brushes may be used, which offers an advantage for substrate feature formation. To demonstrate the three-dimensional (3-D) film structure and show the potential of this system toward applications such as structure generation, the PDMS patterns were transferred to the underlying substrate to fabricate nanoscale features with a feature size of ~14 nm.