The homogeneous structure, and inherent tunability, of molecular glasses makes them particularly interesting for applications in material science and manufacturing. A glass is a nonequilibrium state where the timescales of relaxation far exceed those of observation, such that the atomic structure resembles that of a liquid but possesses the mechanical strength of a solid. In this dissertation, the focus is on the tuning and manipulation of organic glasses, particularly those formed by physical vapor deposition, as well as a polymer glass. Organic glass films formed by physical vapor-deposition have demonstrated remarkable thermophysical properties relative to those formed by conventional liquid cooling and aging techniques, and can be tuned by deposition parameters. In the first part of this work, we utilize a computational procedure that closely mimics the vapor deposition process to examine how the mobile surface of the film influences the characteristics of the resulting films. An all-atom model of ethylbenzene was used to study the substrate temperature dependence of molecular orientation and, by treating ethylbenzene as a simple semiconductor, the corresponding effect vapor deposition has on charge transport properties of the film. This is the first computational atomistic study of an experimentally formed vapor-deposited glass, which demonstrated that with vapor deposition the charge transport properties can be tuned along with providing further evidence that surface relaxation during deposition dictates the resulting average molecular orientation within the film. We then use a coarse-grained model of azobenzene along with an algorithm imitating the photoisomerization reaction to explore the photostability of vapor deposited films. Our results, which are in qualitative agreement with experimental results for the azobenzene derivative disperse orange 37, indicate that the films formed with higher density also have a significant increase in photostability. Continuing the exploration of the photoisomerization response in a glassy medium, we demonstrate that the photoisomerization of a molecularly thin layer within a polymersome, which is assembled from a hydrophilic-azobenzene-hydrophobic diblock copolymer, can reversibly disrupt a glassy matrix to enable leakage in an otherwise sealed membrane via “photo-softening”. Finally, we explore how the location of a ethynyl groups within molecular glass photoresist can affect the glass and structural properties of the material as well as potential confinement effects on the structure.