The Gay-Berne model for liquid crystals in the presence of a substrate surface is studied using the hybrid Monte Carlo method. A simple non-mean-field substrate-molecule potential is proposed to describe the effects of rubbed polymer-coated substrates on the liquid crystals. Effects of the substrate surface on the bulk alignment of the liquid crystals are studied. It is found that the bulk pretilt angle is controlled by the surface through the orientation of the adsorbed liquid crystal monolayer. This is consistent with the results of recent experimental studies.