Ion implantation into silica followed by thermal annealing is an established growth method for Si and Ge nanocrystals. We demonstrate that growth of Group IV semiconductor nanocrystals can be suppressed by co-implantation of oxygen prior to annealing. For Si nanocrystals, at low Si/O dose ratios, oxygen co-implantation leads to a reduction of the average nanocrystal size and a blue-shift of the photoluminescence emission energy. For both Si and Ge nanocrystals, at larger Si/O or Ge/O dose ratios, the implanted specie is oxidized and nanocrystals do not form. This chemical deactivation was utilized to achieve patterned growth of Si and Ge nanocrystals. Si was implanted into a thin SiO2 film on a Si substrate followed by oxygen implantation through an electron beam lithographically defined stencil mask. Thermal annealing of the co-implanted structure yields two-dimensionally patterned growth of Si nanocrystals under the masked regions. We applied a previously developed process to obtain exposed nanocrystals by selective HF etching of the silica matrix to these patterned structures. Atomic force microscopy (AFM) of etched structures revealed that exposed nanocrystals are not laterally displaced from their original positions during the etching process. Therefore, this process provides a means of achieving patterned structures of exposed nanocrystals. The possibilities for scaling this chemical-based lithography process to smaller features and for extending it to 3-D patterning is discussed.