Nanometer-scaled thin films of molecular glasses have been widely applied in photovoltaics, organic light emitting diodes, protective coatings and nano-imprint lithography. Studies show that thin films exhibit enhanced overall dynamics, which may affect the stability of thin films produced by physical vapor deposition. Developing a systematic study on the effect of film thickness and the nature of interface interactions (at free surface and film/substrate interface) can therefore help understand how stability of a vapor deposited thin film changes according to its dynamics. In this thesis, I will firstintroduce the construction and operation of an ultra-high vacuum physical vapor deposition setup that allows for a high-throughput preparation of vapor deposited glasses with different substrate temperatures while sharing similar thicknesses. This setup facilitates studies on the structural properties of vapor deposited thin films, such as morphology and anisotropy. The mass density of vapor deposited glasses of various thicknesses, as a measure of their thermodynamic stability, was investigated on thin films of vapor deposited glasses. Results show that the density of vapor deposited glasses formed under certain conditions exceeds the stability of a limiting equilibrium configuration state, i.e. supercooled liquid. The formation of a high-density liquid state has been hypothesized but had not been experimentally identified in the past. I further demonstrated that by altering the supporting substrate interactions of a vapor deposited film to enhance the degree of interactions between the film and the substrate, the degree of stability can be further improved. Preliminary data found that the kinetic stability can also be improved when a weakly interacting substrate is replaced with neutral substrate. These studies may not only inspire new strategies for industrial applications, but also help elucidate the fundamentals of the dependence of glass stability on film dynamics in molecular glass systems.