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We report on a study of molecular modifications of the electronic characteristics of single-walled carbon nanotube (SWNT) field-effect transistors (FETs) through insertion of different organic self-assembled monolayers (SAMs) between the SWNT and an electrode. The changes induced by the molecular interface were elucidated using a device structure created by directed assembly of a single SWNT over three prepatterned electrodes, one of which had a SAM deposited via dip-pen nanolithography. The resulting direct comparison of two FETs sharing the same SWNT revealed pronounced modification of the transfer characteristics, on/off ratio, and threshold voltages due to the SWNT/molecule/metal junction. The effects are attributed primarily to the alteration of the electronic bands in the Au electrode and the SWNT, and the resulting changes in the effective Schottky barrier height/thickness, by the ordered and well-aligned molecular SAM.