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This paper presents three-dimensions finite element analysis of 2.45 GHz microwave ablation for plagued coronary artery treatment. Any narrowing or blockage of the coronary arteries reduces blood supply to the heart tissue, following by reducing an amount of delivered oxygen and nutrients. This phenomenon inhibits a normal function of the heart muscle. In this research, we propose an application of finite element method to analyze and simulate a microwave ablation process on the blockage or plagued coronary artery. The investigation emphasizes on a reduction of plague or fat size that fixed around a coronary wall when heating by microwave thermal ablation. The simulation results of 3D analysis show the characteristic of temperature distribution in the coronary artery and a destructive area of plaque. 10 Watts of emission power at temperature 95 °C is used as a preliminary value. The simulation found that 3.21 mm3 of plaque size can be destroyed with 10 s. These obtained results usefully guide us to develop and more investigate on a further system in the future.