A method for optically controlling an atomic force microscope (AFM) includes acquiring an optical image of a sample using an optical imaging device, identifying a feature of interest on the sample using the optical image, acquiring a high resolution AFM image of the sample using an AFM imaging device, the AFM imaging device comprising a cantilever having a tip, overlaying the AFM image with the optical image at the feature of interest, and positioning the probe tip over the feature of interest using the optical image.