Transcranial Magnetic Stimulation (TMS) is a technique to stimulate the brain non-invasively. The applications range from accurate localization of the primary motor areas to potential treatment of disorders such as tinnitus, severe depression, and pain. Stereotactic guidance requires individual MR images of the subject's head, which is in some applications typically omitted due to financial motivations. In this paper, we introduce a method that offers improved TMS pulse targeting also to those subjects who do not have MR examinations. A probabilistic brain model was constructed by spatially normalizing the locations of the functional brain areas in a study population, and modeling the distributions and estimates of the locations of the functional brain regions using probabilistic methods. The application of the probabilistic brain model to the target subject was based on a point set determined from the scalp and facial skin of the target subject. The methods were evaluated using data from four functional brain areas from 56 healthy subjects. The accuracy of the estimates of the locations of the functional brain regions was about nine millimeters.