We report a novel method for obtaining ordered arrays of self-assembled Ge nanowires (NWs) using Au seed catalysts, with the latter deposited using a focused ion beam (FIB). For this purpose we apply a three-step process involving first FIB nanopatterning, a second step of AuSi seed formation during UHV annealing, and third the nucleation and growth of Ge NWs by combining molecular-beam epitaxy (MBE) and the vapor-liquid-solid (VLS) process. We show that FIB allows for the local implantation of Au in the areas impacted by the ion beam; the implanted Au evolves during annealing into AuSi clusters, serving as nucleation seeds for the nucleation and growth of Ge NWs. We thus prove that FIB with gold ions is a successful method to obtain gold-catalyzed self-assembled nanowires. We obtain Ge NWs of homogeneous dimensions and oriented in-plane along  directions, as a consequence of a strain-driven process. Wire kinking is governed by surface morphological features. Based on our experimental results, we elaborate on the general mechanisms of MBE growth of quantum wires under epitaxial strain, which we exemplify for Ge NWs on Si(001) but hold for many other lattice-mismatched semiconductor material combinations. © 2011 American Chemical Society.