Cadmium selenide nanocrystal quantum dots (NC-QDs) are site-selectively synthesized by sequential ion beam implantation of selenium and cadmium ions in a SiO2 matrix through submicrometer apertures followed by a rapid thermal annealing step. The structural and optical properties of the NC-QDs are controlled by the ion fluence during implantation and the diameter of the implantation aperture. For low fluences and small apertures the emission of these optically active emitters is blue-shifted compared to that of the bulk material by >100 meV due to quantum confinement. The emission exhibits spectral diffusion and blinking on a second time scales as established also for solution-synthesized NC-QDs.