1. A method for observing a feature within a substrate using a charged particle beam system, comprising: (a) directing an ion beam toward the substrate to expose a cross section including the feature to be observed; (b) directing an electron beam toward the cross section to form an electron beam image of the cross section; (c) analyzing the electron beam image of the feature to determine a position, size, or orientation of a subsequent cross section to be exposed; (f) repeating steps (a) through (c), in which in at least one of the subsequent steps of directing an ion beam to expose a cross section, the position, size, or orientation of the cross section is adjusted in response to the analysis of the electron beam image of the feature.