Predicting the microstructures’ replication in injection-molded parts is challenging due to the large scale difference between macro- and microscale features, requiring significant computational time. To address this, a two-step simulation strategy is proposed: first, simulating the macro-cavity using Moldflow, and then applying the results as boundary conditions for the micro-cavity simulation in COMSOL Multiphysics. The behavior of the polymer melt at the microscale differs from that at the macroscale due to effects like melt-mold surface tension, polymer no flow temperature and melt-mold heat transfer coefficients. These factors are incorporated into the COMSOL model to better predict flow dynamics at the microscale. Experimental tests were conducted to evaluate these effects, comparing numerical results with experimental data under various conditions. This work demonstrates the potential of the model to improve the accuracy of microstructure replication in injection molding.