High intensity focused ultrasound (HIFU) has a great potential for the treatments of stones and/or tumors. In HIFU therapy, respiratory organ motions make it difficult to locate the HIFU focus onto the focal lesions and the risk for damaging the surrounding healthy tissues could be increased. Therefore, we have developed the ultrasound guided motion tracking systems for the moving organs, such as kidneys and livers. Here, the changes of the image patterns seriously deteriorate the motion tracking performance for the focal lesions. To cope with this problem, we proposed a novel motion tracking method to switch templates in accordance with the organ positions in the body. Our method works robustly, even if the image patterns change in accordance with the respirations. Experimental results show the validity of our proposing motion tracking method for the kidneys and livers.