Helium Ion Microscopy is known for its surface sensitivity and high lateral resolution. Here, we present results of a Helium Ion Microscopy based investigation of a surface confined alloy of Ag on Pt(111). Based on a change of the work function of 25 meV across the atomically flat terraces we can distinguish Pt rich from Pt poor areas and visualize the single atomic layer high steps between the terraces. Furthermore, dechanneling contrast has been utilized to measure the periodicity of the hcp/fcc pattern formed in the 2–3 layers thick Ag/Pt alloy film. A periodicity of 6.65 nm along the View the MathML source〈11¯2〉 surface direction has been measured. In terms of crystallography a hcp domain is obtained through a lateral displacement of a part of the outermost layer by View the MathML source1/3 of a nearest neighbor spacing along View the MathML source〈11¯2〉. This periodicity is measured with atomic precision: coincidence between the Ag and the Pt lattices is observed for 23 Ag atoms on 24 Pt atoms. The findings are perfectly in line with results obtained with Low Energy Electron Microscopy and Phase Contrast Atomic Force Microscopy.