Atrial fibrillation (AF) is the most prevalent arrhythmia of the heart, originating usually from ectopic atrial activity of the pulmonary veins. In recent technology, RF ablation has been part of clinical practice for more than two decades and has become an important treatment option for most clinically relevant cardiac arrhythmias . The electrical isolation by ablation of the pulmonary veins (PVs) in the left atrium (LA) of the heart has been proven as an effective cure of atrial fibrillation (AF). The advantage of HIFU is that it could cause deep tissue lesions without damaging intervening tissues and prevent from thrombosis. Thus, it may lead to reducing the risk of stroke. The computer model uses the Pressure Acoustics, Frequency Domain interface to model the stationary acoustic field. The wave equation solved is the homogeneous Helmholtz equation in 2D axisymmetric cylindrical coordinates. With calculated acoustic pressure field, the generated heat combines with the Pennes’ Bioheat Transfer equation to solve the temperature field. The use of extracorporeal HIFU ablation has a problem of vibration motion of heart and it causes focal energy unfocused. The results showed the impact of the thickness of traversing medium to the focal area and heating power with pulse time on the focal area. The varying thickness is to simulate vibration of heart motion. Frequency ranging from 1 MHz to 4 MHz and different geometrical configurations are studied. The preliminary computer modeling and test are feasible. There are in consistent.