In this study of nanopatterned helical poly(benzyl-l-glutamate) (PBLG) brushes, rod-type brush arrays were fabricated via an integrated process of high-resolution lithography and surface-initiated vapor deposition polymerization (SI-VDP). "Nanospikes" of polymer brushes with spacings of less than 100 nm were produced. The topology and areal behavior of the resulting patterned rod-like brushes were analyzed and compared with patterned coil-type brushes. A geometric study of these self-assembled "nanospikes" was carried out, and their cross sections were investigated via focused ion beam (FIB) and scanning electron microscopy (SEM). Furthermore, the presence of poly(N-isopropylacrylamide) (PNIPAM) brushes in unpatterned regions was shown to inhibit undesired "inter-spike" bridging of the PBLG brushes, resulting in more well-defined nanostructures. It was shown that rod-like polypeptide brushes are capable of self-segregation and become arranged vertically without any external support from their surroundings, to form a rod bundle end-point functional topography that could provide possible pathways for studies of model biological surfaces, directed assembly of nanoparticles, or binary mixed brush surfaces with dual properties.