Nanotechnology-based applications of block copolymers (BCPs) require a detailed understanding of microphase separation in thin films during processing. Solvent annealing is a widely employed method for BCP thin films. Quantification of microphase separation is an empirical challenge due to the nature of the buried interface and the scale of temporal dynamics. Several modeling-based approaches have been attempted, but they shed little light on capturing the overall dynamics and interactions that contribute to domain formation in BCP thin films. For the first time, we report in this article a systematic coarse-grained (CG) molecular dynamics (MD) approach that addresses both the ordering and the morphological evolution in solvent swollen thin BCP films. In this study, for an inherently lamellar BCP system, we found that a slight change in relative solvent-block interactions can generate a variety of morphologies including cylindrical, lamellar, and other transient morphologies. In addition, we correlate the profound impact of solvent quality on the interfacial and polymer chain properties in thin films. In addition, we show that the substrate can direct the preferential segregation of blocks and hence align the nanodomains in a well-defined direction. The approach outlined in the present work offers a crucial tool for experimentalists for selection of solvents and substrate types for design of BCP thin films for a variety of applications. It is anticipated that this study will aid the development of effective strategies for morphology selection and provide a recursive scientific tool for appropriate solvent and substrate choices for BCP thin film processing.