Polystyrene-polymethylmethacrylate (PS-PMMA) block copolymers are well known to exhibit microphase separation to form a series of regular structures with local periodic arrangements of the blocks. By developing films of PS-PMMA within topographically patterned silicon (100) substrates (with photolithographically defined rectangular channels of depth 60 nm and widths 166 – 433 nm) these irregular arrangements form highly periodic structures where the features are parallel to the side walls of the channels. However, the use of silicon substrates leads to problems in processing of these films. PS-PMMA does not wet the surface, and this results in island formation on flat substrates. On channel etched substrates this phenomena ensures that the thickness of the films is irregular and poorly defined alignment is seen. Detailed considerations of this polymer system suggest that feature sizes below 25 nm are not realisable. The results suggest other copolymer systems should be studied.