Self-assembled monolayer (SAM) films chemisorbed onto polycrystalline gold substrates have been shown to be effective targets in ion surface collision investigations. One concern has been whether localized defect sites within SAM films (pinholes) influence the amount of ion neutralization that occurs at the surface. Two molecular ion probes, benzene and DMSO-d 6, are employed to measure the degree of neutralization of a selected monolayer. In this investigation, the behavior of these probes upon collision with SAM surfaces composed of CH3(CH2)3S−Au (C4), CH3(CH2)17S−Au (C18), and CF3(CF2)7(CH2)2S−Au (CF) is compared to the behavior of the same SAM surfaces after potential defect sites have been modified by electrodeposition of poly(phenylene oxide). Plots of total ion current vs time show no change in the scattered ion efficiency as a result of the chemical treatment for any of the monolayer films, even in the case of C4 where the CV electrodeposition experiments indicate exposed gold. The results indicate that neutralization of the ion beam that occurs for each SAM film is not a result of the presence of defect sites within the monolayer films. Furthermore, the results also suggest that the C18 and CF surfaces used routinely in surface-induced dissociation experiments in this laboratory do not contain a significant number of defect sites that expose gold.