Efforts in the interdisciplinary field of bioengineering have led to innovative methods for investigating the complexities of cell responses in vitro. These approaches have emphasized the reduction of complex multicomponent cellular microenvironments into distinct individual signals as a means to both (a) better construct mimics of in vivo microenvironments and (b) better deconstruct microenvironments to study them. Microtechnology tools, together with advances in biomaterials, have been fundamental to this progress by enabling the tightly controlled presentation of environmental cues and the improved systematic analysis of cellular perturbations. In this review, we describe bioengineering approaches for controlling and measuring cell-environmental interactions in vitro, including strategies for high-throughput analysis. We also describe the mechanistic insights gained by the use of these novel tools, with associated applications ranging from fundamental biological studies, in vitro modeling of in vivo processes, and cell-based therapies.