Ion bombardment is frequently used in the preparation of thin foils of a variety of materials for analysis by transmission electron microscopy (TEM) and related techniques. We have studied in detail the effects of such specimen preparation techniques on nanometre-sized cavities in silicon by comparing ion-beam milled cross-sectional specimens with those prepared using a small-angle cleavage technique. The cavities have been formed by a prior implantation of energetic helium ions and a high-temperature anneal. In the specimens prepared by ion-beam techniques in two different commercial systems, there is a clear effect on the small cavities. Specifically, the cavities are observed to migrate away from the original surface at both room temperature and liquid nitrogen temperature. The effect is discussed in the context of the interaction of the cavities with mobile vacancies and interstitials injected by the ion bombardment. We believe this to be an important effect that must be taken into account when using TEM techniques to study defects in semiconductors.