We have investigated the changes produced in single-element and two-layer transmission electron microscope (TEM) specimens irradiated by an intense nanometer-sized electron probe, such as that produced in a field-emission or aberration-corrected TEM. These changes include hole formation and the accumulation of material within the irradiated area. The results are discussed in terms of mechanisms, including electron-beam sputtering and surface diffusion. Strategies for minimizing the effect of the beam are considered.