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A three-dimensional numerical model is developed to simulate the mold filling behavior in the plastic encapsulation of microchips. The conventional Hele–Shaw approximation is inadequate to analyze a complex molding compound flow behavior with multiple microchips in a single cavity. The developed numerical algorithm is based on the finite difference method combined with the robustness of volume of fluid volume-tracking method to solve the two-phase flow field in complex mold and die geometries. Twelve dies are arranged in a matrix-array in a single mold cavity. Short-shot experimental data are used to validate the numerical results for the melt flow front at different flow times. Close agreement between the experimental data and the numerical results demonstrates the applicability of the present computational model for the simulation of practical epoxy molding compound encapsulation.