Polymer brushes covalently attached to surfaces have been comprehensively studied for the last two decades since they can effectively transform surface properties for a variety of applications. However, the majority of previous studies have been focused on coil-type polymer brushes, so there is a lack of understanding in the behavior and molecular organization (e.g. conformation) of the equally important rod-type brushes when subjected to external factors such as solvent conditions or temperature. In this study, we found that for polypeptide rod-type brushes the polymer tilt angle from the surface normal changed as a function of brush thickness. Moreover, the number and nature of rod assemblies decreased while the size increased with increasing brush thickness. We showed that rod organization and orientation was strongly dependent on the conditions of a quenching process, depending on factors such as solvent miscibility and extraction rate. We also demonstrated polymer rigidity was crucial to the vertical orientation of the polypeptide. Additionally, polypeptide brushes can induce a change in liquid crystal (LC) orientation through a dispersion interaction, and the LC orientation was also proportional to the tilt of the polypeptide. Moreover, in mixed rod-coil brushes, before solvent quenching, coil brushes decreased the polypeptide tilt angle from the surface normal, resulting in a higher film thickness while after solvent quenching, coil brushes increased the number, but lowered the size of rod assemblies. We also studied nanopatterned polypeptide brushes prepared with electron beam lithography. Polypeptide brushes formed well-defined nanostructures inside pattern boundaries. Both the number of rod assemblies and brush thickness increased with pattern size. When the distance between adjacent patterns was comparable to polymer length, polymer bridges formed due to the interaction between polymer chains of adjacent patterns. The polymer bridges were alleviated by the addition of coil brushes into the otherwise empty areas. Mixed rod-coil brushes of mesogen-jacketed liquid crystalline polymer (MJLCP) and fluorinated polymer was studied. The high immiscibility between the polymers was crucial to the formation of rod assemblies whose size increased with increasing MJLCP thickness. The number of rod assemblies increased with thicker fluorinated brushes. Surface morphology can be tuned by controlling thickness of the two polymers. We also demonstrated coil brush synthesis without a typical deoxygenation step via surface initiated- single electron transfer-living radical polymerization (SI-SET-LRP). Various polymers and brush architectures could be produced with this method.