[en] With the decreasing size of devices, the ability to organize materials and control their physical properties through spatial and morphology manipulation becomes critical. Here, we show that the nature of the organic functional group at the top surface of the self-assembled monolayers can strongly influence the growth of a metallic thin film on the monolayer, as a chemical reaction may occur at the interface. We have sputtered Permalloy (Ni₇₉Fe₂₁) on patterned templates of polar and nonpolar self-assembled monolayers. Uniform film formation is observed on polar regions, and cluster/dropletlike structures are formed on the nonpolar regions. A similar behavior in morphology is observed for the deposition of Permalloy on a substrate having single component self-assembled monolayers. Magnetic measurements reveal that Permalloy exhibits a superparamagnetic behavior when deposited on a nonpolar self-assembled monolayer substrate, whereas a ferromagnetic behavior is observed for Permalloy deposited on a polar self-assembled monolayer substrate. Thus, a systematic deposition of Permalloy on polar and nonpolar self-assembled monolayers allows a control on morphology and the magnetic properties due to the difference in wettability of the terminal organic functional groups of the self-assembled monolayers