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Molecular dynamics simulations are used to model the formation of deep crystalline damage during the low‐energy ion bombardment of semiconductor crystals. For beams of heavy ions at energies below a kilovolt, the average penetration range of the simulated trajectories is only a few nanometers. However, a small, but significant, fraction of the ions are found to scatter into 〈011〉 axial channels through which they propagate tens of nanometers below the surface. A model is developed to convert the simulated ion channeling probabilities into predictions of optical damage as a function of depth in the crystal. The results are used to explain the recent measurements of anomalous degradation of deep quantum wells during dry etching of III–V semiconductor heterostructures. The model is also used to evaluate several strategies intended to avoid this unintentional ion channeling and to reduce the creation of deep damage during low‐energy ion bombardment.