The fabrication of NCs is carried out using an innovative method, ultra-low energy (≤5 keV) ion implantation (ULE-II) into thin (6-9 nm) HfO2–based layers in order to form after subsequent annealing a controlled 2D array of Si NCs. The implantation of Si into HfO2 leads to the formation of SiO2–rich regions at the projected range due to the oxidation of the implanted Si atoms. This anomalous oxidation that takes place at room temperature is mainly due to humidity penetration in damaged layers. Different solutions are investigated here in order to avoid this oxidation process and stabilize the Si-phase. Finally, unexpected structures as HfO2 NCs embedded with SiO2 matrix are obtained and show interesting memory characteristics. Interestingly, a large memory window of 1.18 V has been achieved at relatively low sweeping voltage of ± 6 V for these samples, indicating their utility for low operating voltage memory device.