We investigated the role of substrate topography on neurite development in pheochromocytoma (PC12 cells) by culturing the cells on substrates having nanoscale pillars and pores. In general, cells on nanopillars and nanopores developed fewer and shorter neurites as compared to cells on smooth substrates. But in comparison between the nanopillars the nanopores, cells on nanopores developed more and longer neurites than cells on nanopillars. These results showed that PC12 cells were spatially aware of the difference in the nanoscale structures of the underlying substrates and responded with differences in neurite outgrowth. This fact suggests the possibility to use nanoscale topographic features to control neurite development in neurons.