The evaluation of a plasma-based atomic layer etching (ALE) approach for native oxide surface removal from Si substrates is described. Objectives include removal of the native oxide while minimizing substrate damage, surface residues and substrate loss. Oxide thicknesses were measured using in situ ellipsometry and surface chemistry was analyzed by x-ray photoelectron spectroscopy. The cyclic ALE approach when used for removal of native oxide SiO2 from a Si substrate did not remove native oxide to the extent required. This is due to the high reactivity of the silicon substrate during the low-energy (<40 eV) ion bombardment phase of the cyclic ALE approach which leads to reoxidation of the silicon surface. A modified process, which used continuously biased Ar plasma with periodic CF4 injection, achieved significant oxygen removal from the Si surface, with some residual carbon and fluorine. A subsequent H2/Ar plasma exposure successfully removed residual carbon and fluorine while passivating the silicon surface. The combined treatment reduced oxygen and carbon levels to about half compared to as received silicon surfaces. The downside of this process sequence is a net loss of about 40 Å of Si. A generic insight of this work is the importance of the substrate and final surface chemistry in addition to precise etch control of the target film for ALE processes. By a fluorocarbon-based ALE technique, thin SiO2 layer removal at the Ångstrom level can be precisely performed from an inert substrate, e.g. a thick SiO2 layer. However, from a reactive substrate, like Si, complete removal of the thin SiO2 layer is prevented by the high reactivity of low energy Ar+ ion bombarded Si. The Si surfaces are reoxidized during the ALE ion bombardment etch step, even for very clean and ultra-low O2 process conditions.