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This document specifies methods for the alignment of the ion beam to ensure good depth resolution in sputter depth profiling and optimal cleaning of surfaces when using inert gas ions in Auger electron spectroscopy (AES) and X-ray photoelectron spectroscopy (XPS). These methods are of two types: one involves a Faraday cup to measure the ion current; the other involves imaging methods. The Faraday cup method also specifies the measurements of current density and current distributions in ion beams. The methods are applicable for ion guns with beams with a spot size less than or equal to 1 mm in diameter. The methods do not include depth resolution optimization.