Using all-atom molecular dynamics simulations, the multilayer adsorption of two single-carbon alkane analogues—methane (CH4) and chloromethane (CH3Cl)—in the liquid phase on a metallic substrate (molybdenum (100) surface) has been studied to elucidate differences in the adsorbed film structure as a function of the overall film thickness, system temperature, substrate mobility, and pairwise substrate interaction potential (Lennard-Jones 12-6 versus embedded atom method versus Lennard-Jones 9-3 “wall” potential, used as a basis for comparison). Simulations suggest a clear predilection to well-ordered packing arrangements dictated by the adsorbate molecular geometry when adsorbed on the flat, featureless Lennard-Jones wall, but adsorption on the atomistic molybdenum substrate exhibits a more complex structure and orientation influenced by the adsorbate molecular geometry but also dependent on the presence or lack of small variations in surface structure caused by substrate mobility and interatomic potential. The result illustrates differences in packing geometry and surface binding energy on very noticeable scales despite the magnitude of surface vibrations allowed.