We have investigated the selective electroless deposition (ELD) of Cu on functionalized self-assembled monolayers (SAMs). Previous studies have demonstrated that Cu deposits on -COOH and -CH3 terminated SAMs using ELD. However, the deposited films were rough and contained irregular crystallites. Further, the copper penetrated through the film. In this Article, we demonstrate that copper can be selectively deposited on -COOH terminated SAMs with improved morphology and without penetration of copper through the organic layer. The method employs a Cu(II) seed layer and an additive, adenine or guanine. We demonstrate the efficacy of the technique on photopatterned -CH3/-COOH SAMs. Copper is observed to deposit only atop the -COOH terminated SAM area and not on the -CH3 terminated SAM. The use of a Cu(II) seed layer increased the Cu ELD rate on both -COOH and -CH3 terminated SAMs. The deposited copper layer strongly adheres to the -COOH terminated SAMs because the copper layer nucleates at Cu2+ -carboxylate complexes. In contrast, the deposited copper layer can easily be removed from the -CH3 terminated SAM surface because there is no specific copper-surface interaction. The additives adenine and guanine mediate the interaction of Cu2+ and the deprotonated -COOH terminated SAMs via the formation of additive-carboxylate complexes. These complexes lead to significantly reduced copper penetration through the SAM. In the case of adenine, the diffusion of copper through the organic film was eliminated this new technique for copper deposition will facilitate the development of inexpensive molecular electronics, sensors, another nanotechological devices.