Directed assembly of nanoscale building blocks such as single-walled carbon nanotubes (SWNTs) into desired architectures is a major hurdle for a broad range of basic research and technological applications (e.g., electronic devices and sensors). Here we demonstrate a parallel assembly process that allows one to simultaneously position, shape, and link SWNTs with sub-100-nm resolution. Our method is based on the observation that SWNTs are strongly attracted to COOH-terminated self-assembled monolayers (COOH-SAMs) and that SWNTs with lengths greater than the dimensions of a COOH-SAM feature will align along the boundary between the COOH-SAM feature and a passivating CH3-terminated SAM. By using nanopatterned affinity templates of 16-mercaptohexadecanonic acid, passivated with 1-octadecanethiol, we have formed SWNT dot, ring, arc, letter, and even more sophisticated structured thin films and continuous ropes. Experiment and theory (Monte Carlo simulations) suggest that the COOH-SAMs localize the solvent carrying the nanotubes on the SAM features, and that van der Waals interactions between the tubes and the COOH-rich feature drive the assembly process. A mathematical relationship describing the geometrically weighted interactions between SWNTs and the two different SAMs required to overcome solvent-SWNT interactions and effect assembly is provided.