Spatially patterned ion beam implantation of 190 keV Co(+) ions into a SiO(2) thin film on a Si substrate has been achieved by using nanoporous anodic aluminum oxide with a pore diameter of 125 nm as a mask. The successful synthesis of periodic embedded Co regions using pattern transfer is demonstrated for the first time using cross-sectional (scanning) transmission electron microscopy (TEM) in combination with analytical TEM. Implanted Co regions are found at the correct relative lateral periodicity given by the mask and at a depth of about 120 nm.