Abstract <p>This work presents a high-throughput microstructure simulation framework for use in the discipline of computational materials science to screen out desirable structures. As motivation, we present a brief study of battery microstructural architecture optimization. Realistic 3D microstructures are reconstructed from voxel data. The voxel data can be easily modified, enabling rapid manipulation and making high-throughput investigation possible. The microstructure-level simulations are made computationally feasible by using the Smoothed Boundary Method to embed complicated microstructures in the computational domain. Additionally, our efforts toward an open-source microscale battery simulation software, titled BESFEM, are previewed.</p> Graphical Abstract <p></p>