Ion beam sputtering of ultrathin film Au coatings used as a physical catalyst for self-organization of Si nanostructures has been achieved by tuning the incident particle energy. This approach holds promise as a scalable nanomanufacturing parallel processing alternative to candidate nanolithography techniques. Structures of 11- to 14-nm Si nanodots are formed with normal incidence low-energy Ar ions of 200 eV and fluences above 2 × 1017 cm-2. In situ surface characterization during ion irradiation elucidates early stage ion mixing migration mechanism for nanodot self-organization. In particular, the evolution from gold film islands to the formation of ion-induced metastable gold silicide followed by pure Si nanodots formed with no need for impurity seeding.