Atomic layer plasma technologies require localizing ions' impact within nanometers up to an atomic layer. The possible way to achieve this is the decrease in the ion energy up to surface binding energy. At such low ion kinetic energies, the impact of different plasma effects, causing the surface modification, can be of the same order as kinetic ones. In this work, we studied the sputtering of amorphous silicon films by Ar+, Kr+, and Xe+ ions at energies of 20–200 eV under the low-pressure inductively coupled plasma discharge in pure argon, krypton, and xenon, respectively, at a plasma density of 1–1.5 × 1010 cm−3. Under the plasma conditions, a high asymmetry of discharge allowed to form ion flux energy distribution functions with narrow energy peak (5 ± 2 eV full width at half maximum). Real time in situ control over the ion composition and flux as well as the sputtering rate (the ratio of the film thickness change to the sputtering time) provided accurate determination of the sputtering yields Y(Ei). It is shown that at ion energy above ∼70 eV, the “classical” kinetic sputtering mechanism prevails. In this case, Y(Ei) grows rather rapidly with ion energy, increasing with the decrease in the ion mass: the closer the ion mass to the target atom mass, the higher the Y(Ei). Below 70 eV, the growth of Y(Ei) strongly slows down, with Y(20eV) being still high (>10−3), indicating the impact of plasma. The obtained trends of Y(Ei) are discussed in light of surface modification studied by atomic force microscopy and angular x-ray photoelectronic spectroscopy.