In this paper, the real geometries of cathode particles are reconstructed using atomic force microscopy (AFM). Finite element analysis of intercalation-induced stress is applied to the reconstructed realistic geometries of single and aggregated particles. The reconstructed particle geometry shows rugged surfaces at the boundary for Li-ion flux, which cause larger surface areas than smooth particles. The finite element model of a LiMn2O4 system is simulated under galvanostatic and potentiodynamic control. To investigate the realistic level of boundary flux at particle scale, macroscale simulation results are also applied to intercalation-induced stress analysis of real cathode particles. The numerical results of intercalation-induced stress show that the von Mises stress is concentrated at sharply dented boundaries due to curvature effects when Li ions intercalate or deintercalate and is an order-of-magnitude higher in realistic particle geometries than the stress in ideal smooth particles. It has also been shown that the stress under potentiodynamic control is higher than the stress under galvanostatic control because the high Li-ion flux at two plateaus in the open-circuit potential of a LiMn2O4 system results from linear voltage sweep. We also present results showing that some mesh architectures are preferred for handling these potentially singular regions.