Transcranial Magnetic Stimulation(TMS) is a noninvasive technique used for treating stroke, Parkinson's disease and depression among others by directly applying magnetic stimulation to the brain. In this system, navigation system that can provide accurate information on location of stimulation is needed for effective TMS because it is critical to stimulate the anatomical location of patient very precisely. In this study, accurate information on location for brain stimulation was obtained from stereo camera image that utilized webcams. Such information on location was used to find precise location for brain stimulation through 3-dimensional visualization of MR image and application of registration.