We show that templating a Si surface with a focused beam of Si2+ or Si+ ions can create suitable nucleation sites for the subsequent growth of self-assembled Ge quantum dots by chemical vapor deposition. To determine the mechanism of patterning we use atomic force microscopy to show that, similar to Ga+ patterning, the formation of a surface pit is required to enable control over Ge quantum dot locations. We find that relatively high implantation doses are required to achieve patterning, and these doses lead to amorphization of the substrate. We assess the degree to which the substrate crystallinity can be recovered by subsequent processing. Using in situ transmission electron microscopy heating experiments we find that recrystallization is possible at the growth temperature of the Ge quantum dots, but defects remain that follow the pattern of the initial implantation. We discuss the formation mechanism of the defects and the benefits of using Si ions for patterning both defects and quantum dots on Si substrates.