The present invention provides a method for optimizing a shaped working beam having a sharp edge for making sufficiently precise cuts and a high beam current for faster processing. An ion beam is directed along an optical column through a reference aperture to form a reference beam that has a preferred shape and an associated reference current. The reference beam is optimized using selected parameters of the optical components within the optical column. The ion beam is then directed through a working aperture to form a working beam for use in a processing application. The working beam has a different shape from the reference beam and an associated working current that is higher than the reference current. The reference aperture and working aperture have at least one corresponding dimension. The working beam is then optimized using the selected optical component parameters used to align and focus the reference beam.