Molecular orientation in organic semiconductors plays a critical role in maximizing external quantum efficiencies of organic light-emitting diodes. It was generally believed that the molecular packing of organic semiconductors is either amorphous or liquid-crystal-like with a preferred molecular orientation distributed uniformly throughout the film. In this paper, however, we report that the orientation of organic molecules in physical-vapor deposited films varies drastically depending on thickness. The thermal stability of the molecular network, measured by its characteristic glass transition temperature, also varies as a function of the film thickness. Based on a two-layered film-structure model, we propose a simple function to quantify the molecular dipole orientation S parameter as a function of film thickness. This function describes well experimental data. In addition to contributing to external quantum efficiency, the molecular orientation parameter S is found to have a strong impact on disruptive change in material density after thermal anneal and glass transition.