Solution casting using a sacrificial template is a simple technique to fabricate vertical arrays of polymer nanotubes. However, because of their close proximity and high aspect ratios, large capillary forces cause nanotubes to cluster as the array dries; researchers often use special drying techniques to avoid this clustering. Here, we exploit the clustering of regioregular poly(3-hexylthiophene) (rr-P3HT) nanotubes in a unique template etching process to create surfaces that exhibit tunable wetting and contact thermal energy transport. Vertical arrays of rr-P3HT nanotubes are cast from solution in nanoscale alumina templates, and a solution etching process is used to partially release the nanotubes from the template. The clustering of rr-P3HT nanotube tips upon template etching produces hierarchical surface structuring with a distinct pattern of interconnected ridges, and the spacing between the ridges increases with increased template etch times. These changes in morphology cause the water contact angle to increase from 141° to 168° as the etch time is increased from 4 to 12 min. When assembled into an interface, the morphological changes cause the thermal contact resistance of the vertical rr-P3HT nanotube arrays to increase linearly at a rate of approximately 6 mm(2)·K/W per 2 min etch interval (after 6 min of etching is surpassed). The effective thermal conductivity of the rr-P3HT nanotube arrays is 1 ± 0.2 W/mK independent of the etch time, which is approximately 5 times higher than the bulk rr-P3HT film value.