This article presents a molecular dynamics simulation of the copper reflow process for the recently developed damascene process, in which copper replaces aluminum as the interconnect material. A deposition simulation is performed, and one of the results from this simulation, namely a morphology with a void defect within the filling trench, is used as the initial morphology for the annealing process. The influence of variations in the annealing process parameters on void filling within the trench and on the copper microstructure is investigated. The article establishes a three-dimensional trench model and also provides deposition and reflow models. The annealing procedure is modeled by employing the Langevin technique to simulate heating and cooling of the thermal layer located beneath the Ti barrier layer which covers the trench. The many-body, tight-binding potential model is adopted to simulate the interatomic force between atoms. The results of this study indicate that the duration for which a constant annealing temperature is maintained plays an important role in determining the success of the reflow process. A short duration fails to produce motion of the atoms located in the trench above the void, and this motionless region of atoms prevents atoms from flowing into the trench to fill the void-The motion trace of trench atoms during the reflow process shows that circular motion is evident in the atoms that are located in the region surrounding the void, while atoms in the region above the void migrate for a long distance in the direction of the void. Finally, it is determined that a longer heating duration is beneficial in improving the microstructure of the interconnects.