Thin films of nematic liquid crystals confined to geometrically as well as chemically patterned substrate at one end and a planar substrate with strong anchoring at the other are studied employing non-Boltzmann Monte Carlo methods. We investigate the effect of temperature on the director structures as the system goes through the isotropic-nematic phase transition. The low temperature results show significant deviations from the phase diagram predicted within the continuum approximation, depicted as a function of the tilt angle at the top substrate and the thickness of the cell. Onset of phase biaxiality is observed at very low temperatures, and it increases as the tilt angle at the top substrate is increased, moving away from the normal to the substrate. A phase shift introduced between the geometrical and chemical patterns at the other end also enhances the phase biaxiality of the system to a fairly high value. This seems to provide a convenient experimentally tunable parameter for controlling the symmetry of the director structures.