In silicon nanocrystal (nc) based metal-oxide-semiconductor (MOS) memory structures a fine control of the Si nc location in the gate oxide is required for the pinpointing of optimal device architectures. In this work, we show how to manipulate and control the depth-position, size and surface density of two dimensional (2D) arrays of Si ncs embedded in thin (<10 nm) SiO2 layers, fabricated by ultra-low-energy (typically 1 keV) ion implantation and subsequent annealing. Particular emphasis is placed upon the influence of implantation, annealing conditions and oxide thickness on the nanocrystal characteristics (e.g. size, density) and the charge storage properties of associated MOS structures. Structural investigation is performed by using specific characterization methods including Fresnel imaging for the measurement of the injection distance between the substrate and the nc band, as well as spatially resolved Electron Energy Loss Spectroscopy using the spectrum-imaging mode of a Scanning Transmission Electron Microscope to evaluate the size distribution and density of the ncs.