In block copolymer (BCP) nanolithography, microphase separated polystyrene-block-polydimethylsiloxane (PS-b-PDMS) thin films are particularly attractive as they can form small features and the two blocks can be readily differentiated during pattern transfer. However, PS-b-PDMS is challenging because the chemical differences in the blocks can result in poor surface-wetting, poor pattern orientation control and structural instabilities. Usually the interfacial energies at substrate surface are engineered with the use of a hydroxyl-terminated polydimethylsiloxane (PDMS-OH) homopolymer brush. Herein, we report a facile, rapid and tuneable molecular functionalization approach using hexamethyldisilazane (HMDS). The work is applied to both planar and topographically patterned substrates and investigation of graphoepitaxial methods for directed self-assembly and long-range translational alignment of BCP domains is reported. The hexagonally arranged in-plane and out-of-plane PDMS cylinders structures formed by microphase separation were successfully used as on-chip etch masks for pattern transfer to the underlying silicon substrate. The molecular approach developed here affords significant advantages when compared to the more usual PDMS-OH brushes used.