Abstract: A method and apparatus for positioning an instrument in a predetermined region within a patient's body is disclosed herein generally having a custom fitted surgical guide template which corresponds to a digital model of the portion of the patient's body. The custom fitted surgical guide template is positionable about a portion of the patient's body surface that is identifiable and unique for each patient which is fixed relative to adjacent anatomical structures. The custom fitted surgical guide may also have at least one instrument guiding mechanism which is positioned to guide an instrument along a predetermined trajectory into the predetermined region within the patient's body. The instrument may be advanced through the instrument guiding mechanism using a steering mechanism regulated by a physiological parameter.