We present findings from a recent molecular dynamics study of multilayer adsorption of tetrafluoromethane (CF4) onto two atomically flat but chemically and structurally different substrates: graphite (hydrophobic) and hydroxylated α-quartz (hydrophilic). Simulations in this study were carried out at temperatures in the range of 60–120K. Subsequent analysis shows that the structure and character of the substrate surface play a large role in whether adsorbed films exhibit packing arrangements that are highly ordered or are subject to a high degree of temperature dependence. Additionally, flexible hydroxyl groups on the surface of hydroxylated α-quartz are shown to arrange themselves in a zig-zag pattern that creates an array of hexagonal domains which determine the allowed CF4 adsorption sites.