Electrically conducting polymers such as polypyrrole (PPy) are important biomaterials in neural engineering applications, including neural probes, nerve conduits, and scaffolds for tissue and nerve regeneration. Surface modification of these polymers can introduce other valuable characteristics for neural interfacing in addition to electrical conductivity, such as topographical features and chemical bioactivity. Here, the patterning of PPy to create topographical cues for cells is reported. In particular, 1 and 2 pm wide PPy microchannels are fabricated using electron-beam (e-beam) lithography and electropolymerization. A systematic analysis of parameters controlling PPy micropatterning is performed, and finds that microchannel depth, roughness, and morphology are highly dependent on the e-beam writing current, polymerization current, PPy/dopant concentrations, and the polymerization time. Embryonic hippocampal neurons cultured on patterned PPy polarize (i.e., defined an axon) faster on this modified material, with a twofold increase in the number of cells with axons compared to cells cultured on unmodified PPy. These topographical features also have an effect on axon orientation but do not have a significant effect on overall axon length. This is the first investigation that studies controlled PPy patterning with small dimensions (i.e., less than 5 pm) for biological applications, which demonstrates the relevance of expanding microelectronic materials and techniques to the biomedical field.