Directed self-assembly of Si containing block copolymers (BCP) is a candidate for next generation patterning technology because it enables both high resolution and high etch contrast. Achieving high resolution requires a high χ parameter. However, it is often difficult to achieve perpendicular patterns by thermal annealing of BCPs with a lower surface energy block, which tends to align with the air interface. New top surface treatment materials that provide a surface energy between those of the blocks have been developed that enable perpendicular pattern alignment with block copolymers that have a low surface energy block.