An improved method and apparatus for imaging and milling a substrate using a FIB system. Preferred embodiments of the present invention use a mixture of light and heavy ions, focused to the same focal point by the same beam optics, to simultaneously mill the sample surface (primarily with the heavy ions) while the light ions penetrate deeper into the sample to allow the generation of images of subsurface features. Among other uses, preferred embodiments of the present invention provide improved methods of navigation and sample processing that can be used for various circuit edit applications, such as backside circuit edit.