Microscopes auto focusing is critically important for a great spectrum of scientific and industrial applications. Finding the best focus position for variety of surfaces under measurement proved to be challenging. In order to provide a rapid and accurate method for microscope focusing positioning, a laser focus deviate system was employed for microscope focusing position. The relationship between focusing sensitivity and the surface under measurement was investigated. First, the laser focus deviate technique is introduced in light of characteristic parameters such as the diameter of the focused spot, the laser wavelength and the distance from the optimal focus. Then, the focusing displacement versus spot position curve fitting is performed for a smooth isotropic surface to directly locate the best focusing position. Following, it is analyzed that when applied to anisotropic and rough surfaces, the centroid of the image spot after reflection/scattering from the surface will deviate from its original light intensity distribution, thus deviate from the calculated optimal focus position and cause focusing errors. Finally, a criterion of weighted light intensity value Q is introduced to achieve fast focusing of anisotropic surfaces in combination with the laser focusing deviate technique. The experimental results show that for a 20× microscope objective system, the focusing accuracy of this focusing positioning method is 1.7 μm on smooth surfaces; and is at the micro meter level for rough surfaces. It basically meets the requirements for rapid, stable and reliable microscope auto focusing needs.