The directed self-assembly (DSA) of block copolymer (BCP) thin films could enable a scalable, bottom-up alternative to photolithography for the generation of substrate features. The PS-b-PDMS (polystyrene-b-polydimethylsiloxane) system is attractive as it can be extended toward very small feature sizes as well as having two blocks that can be readily differentiated during pattern transfer. However, PS-b-PDMS offers a considerable challenge because of the chemical differences in the blocks which lead to poor surface-wetting, poor pattern orientation control, and structural instabilities. These challenges can be mitigated by careful definition of the interface chemistry between the substrate and the BCP. Here, we report controlled pattern formation in cylinder forming PS-b-PDMS system by use of a carefully controlled PDMS brush. Control of the brush was achieved using exposure to UV−O3 for varying time. It is demonstrated that this treatment enhances surface wetting and coverage of the BCP. The modified brushes also enable DSA of the BCP on topographically patterned substrates. UV−O3 exposure was also used to reveal the BCP structure and provide an in situ “hard mask” for pattern transfer to the substrate.