Secondary ion mass spectra of self-assembled monolayers (SAMs) of the thiol-containing molecules (η5-C5H5)-Fe[(η5-C5H4)CO(CH2)10SH] (I) and C18H37SH (III) and their isotopically labeled analogs (η5-C5D5)Fe[(η5-C5D4)CO(CH2)10SH] (II) and C18D37SH (IV) on polycrystalline Au films are presented. These spectra were taken using a VG IX70S magnetic sector SIMS instrument. Peaks corresponding to parentlike ions [M + H]+, [M -H]+, or [M + Au]+ with the expected isotopic shifts for I-IV were detected, verifying the presence of intact molecules of I-IV on the Au films. Molecular fragments of I-IV were also observed, e.g. [(C5H5)Fe]+ for SAMs of I and [(C5D5)Fe]+ for SAMs of II. Importantly, the use of SIMS to map the distribution of species I on a Au microwire array (wires 4.8 pm wide, separated by 1.2 pm on a Si3N4 substrate) is demonstrated. Comparison of maps of Fe+ and the molecular fragment [(C5H5)Fe]+ with Au+ and Si+ maps shows that I is found only on Au and not the Si3N4 substrate. The elemental and molecular ion maps represent the detection of 300 million molecules of I per microwire at a lateral resolution of less than 1 μm. Furthermore, each map covered 2500 μm2 and was acquired in less than 40 s; comparable element mapping of Au microwire by Auger electron spectroscopy requires hours.