Generally, the present invention is directed to a method and system for a aligning surgical guide instrument over a burr hole in a patient's body. More particularly, the present invention is directed to a stand-alone instrument guidance unit that is attachable to a patient's skull. Adjustments of a surgical instrument can be made in x, y, z, and angular directions using the system and method of the present invention. In one aspect of the present invention, an instrument guide unit includes an instrument guide for guiding a surgical instrument into the body of a patient and a base unit operative to be secured to the body in an area in which surgery is to occur. The base unit is coupled to the instrument guide. An adjustment mechanism, coupled to the base unit and the instrument guide, is operative to adjust the instrument guide in lateral directions with respect the surface of the area. The adjustment mechanism is operative to adjust the instrument guide in x and y directions. The adjustment mechanism includes an x direction control mechanism for adjusting the instrument in an x direction and a y direction control mechanism for adjusting the instrument in a y direction. The y direction control mechanism may be coupled to the x direction control mechanism. The positional movement of the surgical instrument in the z direction may be tracked by sensing the location of a transducer coupled to the surgical instrument.