We have achieved three-dimensional imaging of decanethiol self-assembled monolayers (SAMs) on metal surfaces by atom probe tomography (APT). The present Letter provides preliminary results on Ni [001] and Au [111], shows the analytical potential of APT analysis of SAMs, and details developments in specimen preparation and in data-treatment methodologies. Importantly, the investigation of the mass spectra from analysis of the SAMs revealed no combination of sulfur and hydrogen at the interface between the metal substrates and the organic materials, potentially providing insight about the bonding of the thiols on the substrate.