Stable glasses can be made through physical vapor deposition when certain deposition conditions are met. The structure and properties of stable glasses are strongly dependent on the equilibrated surface structure and dynamics during deposition, regulated by surface mediated equilibrium. Hence, studies of surface properties, such as comparing surface relaxation times and surface coordination states with those of the bulk, measuring the length scale over which surface properties can persist into the films, and how these quantities can be altered, become very important in controlling the properties of vapor deposited glasses. This thesis presents several research projects on the effects of molecular structures and deposition conditions on the packing and stability of vapor deposited glasses. To understand the distinct properties of glass surface, indirect experiments on thin film relaxations dynamics were performed. In addition, we have used light and chemical modifications to change the surface structure and dynamics, studying those effects on glass stability. In Chapter 2, amorphous selenium (a-Se) stable glasses were made in dark and under above-bandgap light. Despite their low relative density, a-Se glasses deposited under light exhibited higher kinetic stability compared to the glasses deposited in dark, which is originated from the highly networked structure inherited from the surface structure under light. Chapter 3 is an extended study of Chapter 2 which determined the degree of light facilitated relaxation in a-Se thin films. Chapter 4 demonstrated an extremely long length scale of bulk to thin film transition in a-Se systems compared to what has been found in organic glasses. This extremely long length scale is likely to be related to the increasing density of three/four-coordinated states in a-Se thin films. Chapter 6 resolved the role of intramolecular degrees of freedom on stable glass formation. Especially, the relationship and distinctions between stable glasses optical birefringence and molecular layering were discussed. These observations are connected to the thickness of the mobile surface layer at various deposition conditions, as well as the role of molecular orientation at the top surface. In Chapter 7, we focused on the how intermolecular interaction and micro-phase separation influence stable glass structure and stability.