We combine scanning tunneling microscopy ͑STM͒ images, density functional theory total energy calculations, and STM simulations to conclusively determine the surface structure of the Y 3 Si 5 ͑0001͒ silicide epitaxially grown on Si͑111͒. We observe, for the same sample, two different types of atomic resolution images exhibiting either p3m or p6 symmetry, in analogy with previous works on similar rare-earth silicide surfaces. We elucidate the long-standing controversy regarding the interpretation of these images by showing that they are mainly related to the registry of the surfacemost Si bilayer with respect to the Si vacancy network located two layers below the surface and, therefore, to the existence of two different buried structural domains. Our results demonstrate an unsual STM depth sensitivity-up to 5 Å-for metallic systems.