The use of low-energy ions in conjunction with molecular beam epitaxy is discussed. Energetic ions can create surface defects; they can also create unwanted bulk defects. In the first part of this paper, we present calculations showing how the partitioning of these two processes depends on incident ion mass and energy. Because epitaxy is a surface process, mediated by particular kinds of surface defects (e.g., adatoms, clusters, steps) it will be strongly influenced by other surface defects (e.g., surface vacancies) created by ion bombardment. Therefore, we are interested in the interaction of these various surface defects. The evolution of these defects manifests itself in changes in surface morphology, which we monitor by reflection high-energy electron diffraction (RHEED). In the second part of this paper, we present two examples of the first such dynamic measurements of surface morphology during ion bombardment and epitaxy: one in which chemically reactive H + ions smoothen static Ge surfaces, and one in which chemically inert Ar + ions roughen static Ge surfaces, but smoothen dynamic (growing) Ge surfaces.