The penetration behavior of thermally evaporated Au on S(CH2) 15CH3, S(CH2)(15)CO2CH3, S(CH2)(15)CO2H, K-modified S(CH2)(15)CO2CH3, and K-modified S(CH2) 15CO2H self-assembled monolayers (SAM) on Au substrates is investigated. Gold is a particularly interesting metal since vapor-deposited Au atoms are known to pass through alkanethiolate SAMs on Au{111} substrates at room temperature. Here we show that it is possible to control Au penetration by adjusting the interactions between terminal groups. It is found that Au atoms evenly penetrate into the CH3 and CO2CH3 films, forming smooth buried layers below the organic thin films. For the CO2H film, although Au atoms can still penetrate through it, filaments and mushroomlike clusters form due to H-bonding between film molecules. In the case of the K-modified CO2CH3 or CO2H films, however, most Au atoms form islands at the vacuum interface. These results suggest that van der Waals forces and H-bonds are not strong enough to block Au from going through but that ionic interactions are able to block Au penetration. The measurements were performed primarily using time-of-flight secondary ion mass spectrometry (ToF-SIMS) and atomic force microscopy (AFM). The combination of these highly complementary probes provides a very useful strategy for the study of metal atom behavior on SAMs.