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Background: Biochemical and biophysical factors jointly regulate the cellular dynamics in many physiological processes. It is therefore imperative to include multiplexed microenvironment cues when employing in vitro cell-based assays to model physiological processes. Methods: To meet this need, we have developed a modular platform of 3D cell culture, Modular Control of Microenvironment for Cell Migration and Culture Assay (MC3A), that incorporates directed chemical and mechanical cues in the forms of chemotaxis and contact guidance, respectively. Taking advantage of the functionalities of MC3A, we study the migration and morphology of breast cancer cells in 3D engineered extracellular matrix (ECM) following a serum gradient for chemotaxis. Results: We show that when chemotaxis is facilitated by contact guidance in the same direction as the serum gradient, cells demonstrate dimensional-reduction in their motility and highly elongated ellipsoidal shape. When the direction of ECM alignment diverges from the direction of serum gradient, chemotactic motion is significantly suppressed, and cells are generally more protrusive and rounded in their morphology. Conclusions: These examples demonstrate MC3A as a powerful tool for engineering complex microenvironments of cells that will advance the state-of-the-art of cell-based analysis in drug development, regenerative medicine, and other research areas in bioengineering.