We propose an original approach called “stencil-masked ion implantation process” to perform a spatially localized synthesis of a limited number of Si nanoparticles (nps) within a thin SiO2 layer. This process consists in implanting silicon ions at ultra-low energy through a stencil mask containing a periodic array of opened windows (from 50 nm to 2 um). After the stencil removal, a thermal annealing is used to synthesize small and spherical embedded nps. AFM observations show that the stencil windows are perfectly transferred into the substrate without any clogging or blurring effect. The samples exhibit a 3 nm localized swelling of the regions rich in Si nps. Moreover, photoluminescence (PL) spectroscopy shows that due to the quantum confinement only the implanted regions containing the Si nps are emitting light.