The effect of electron cyclotron resonance plasma cleaning (100)Si surfaces with low energy Ne, Ar, and Xe ions is studied byinsitux‐ray photoelectron spectroscopy, high‐resolution cross‐sectional transmission electron microscopy, atomic force microscopy, and measurement of both the single‐surface reflectance and the modulated optical reflectance. Photoemission spectra show that complete removal of all surface contaminants with oxygen atoms knocked‐in from the original native Si oxide and noble gas atoms implanted into the Si substrate are a common characteristic of this plasma cleaning process. The oxygen concentration appears to decrease with ion energy for all three ions, whereas the noble gas concentration is inversely proportional to the ion mass and essentially independent of the ion energy. This low energy ion bombardment sputters the surface causing only point defects with Ne ions, formation of a continuous thin amorphous overlayer with either Ar or Xe ions, and in addition, occasional subsurface planar defects with Xe ions alone. The original smoothness of the monocrystalline Si surface is maintained with Ne ions, while an increase in surface roughness accompanies the amorphization caused by Ar and Xe ions. The magnitude of the roughness, which depends more on the energy than on the mass of either ion is insufficiently small to account for a change in specularity at visible wavelengths. An increase in both the single‐surface reflectance and the modulated optical reflectance is always observed after the plasma exposure and is shown to provide a sensitive measure of these changes in surface morphology with the latter technique being a somewhat more sensitive gauge of these effects.