Atrial fibrillation (AF) is the most prevalent arrhythmia of the heart, originating usually from ectopic atrial activity of the pulmonary veins. It is the most common sustained cardiac arrhythmia, occurring in 1–2% of the general population. 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 high intensity focused ultrasound (HIFU) treatment modality has been proposed in 1995 and is not as popular as RF at present, however HIFU one can cause deep tissue lesions without damaging intervening tissues and wide in treatment than RF one. It is now well known that the pulmonary veins (PVs) play a critical role in the initiation and maintenance of atrial fibrillation (AF). Circular electroporation ablations are normally used with different electrode devices for near PVs. Lesion depth is one of factors in creating better catheter ablation for AF treatments. Similarly, HIFU may generate circular ablations. However, the oscillation or rhythm of heart make the HIFU thermal ablation become difficult to complete. This paper would like to discuss computer simulation in the issue of ablations.