Surface vacancy and adatom clusters have been created on Ge(001) by bombarding the surface with 800 eV argon ions at various substrate temperatures ranging from room temperature to 600 K. The vacancies preferentially annihilate at the ends rather than at the sides of the dimer rows, resulting in monolayer deep vacancy islands which are elongated in a direction of the dimer rows of the upper terrace. As vacancy islands nucleate and expand, the dimer rows in neighbouring vacancy islands need not, in general, align with each other. An antiphase boundary will develop if two growing vacancy islands meet, but their internal dimer rows are not in the same registry. In contrast to Si(001), where only one type of antiphase boundary is found, we have found three different types of antiphase boundaries on Ge(001). Higher dose (> several monolayers) room temperature ion bombardment followed by annealing at temperatures in the range 400¿500 K results in a surface which contains a high density of valleys. In addition to the preference for the annihilation of dimer vacancies at descending versus ascending steps we also suggest that the development of antiphase boundaries drives the roughening of this surface. Finally, several atomic rearrangement events, which might be induced by the tunneling process, are observed after low-dose ion bombardment at room temperature.