We have explored the use of mold coatings and optimized processing conditions to injection mold high aspect ratio nanostructures (height-to-width >1) in cyclic olefin copolymer (COC). Optimizing the molding parameters on uncoated nickel molds resulted in slight improvements in replication quality as described by height, width and uniformity of the nanoscopic features. Use of a mold temperature transiently above the polymer glass transition temperature (Tg) was the most important factor in increasing the replication fidelity. Surface coating of the nickel molds with a fluorocarbon-containing thin film (FDTS) greatly enhanced the quality of replicated features, in particular at transient mold temperatures above Tg. Injection molding using the latter mold temperature regime resulted in a bimodal distribution of pillar heights, corresponding to either full or very poor replication of the individual pillars. The poorly replicated structures on nickel molds with or without FDTS coatings all appeared fractured. We investigated the underlying mechanism in a macroscopic model system and found reduced wetting and strongly decreased adhesion of solidified COC droplets on nickel surfaces after coating with FDTS. Reduced adhesion forces are consistent with lowered friction that reduces the risk of fracturing the nanoscopic pillars during demolding. Optimized mold surface chemistry and associated injection molding conditions permitted the fabrication of square arrays of 40 nm wide and 107 nm high (aspect ratio >2.5) pillars on a 200 nm pitch.