Transmission ion channeling is a powerful analytical tool for determining surface structure, but involves special equipment and sample preparation considerations. We describe an ultrahigh vacuum structural analysis and sample preparation facility for transmission ion channeling studies of monolayer films on clean semiconductor surfaces. After samples are cleaned and films deposited, they can be moved under vacuum and investigated using low energy electron diffraction, Auger electron spectroscopy, atomic resolution scanning tunneling microscopy, or, using an ion scattering chamber attached to a beamline of a 3.5 MeV Van de Graaff accelerator, transmission ion channeling. Transmission channeling can determine the bonding position of adatoms to typically 0.1 Å resolution, and is one of the few techniques able to measure reconstruction at a buried interface or to detect the presence of order in the midst of disorder. These aspects of the technique are illustrated by a site determination of a monolayer of Sb deposited on Si(100) and by a determination of the pseudomorphic fraction of thin Ge films deposited on Si(100) at low growth temperatures.