Prussian-blue analogues (PBA) are a family of molecule-based magnetic compounds of general formula AxMy[M(CN)6]z, whose magnetic properties can be tuned by an external stimulus. This tunability makes PBA good candidates for their integration into new electronic or spintronic devices. As a previous step to accomplish this integration, PBA need to be deposited onto surfaces in controllable ways and if possible into specific positions on the surface. Even though the study of PBA has traditionally been limited to bulk, lately they have also been processed as nanoparticles (NPs). Here an efficient approach is presented for the accurate deposition and organization of PBA-NPs of different sizes (from 6 to 25 nm) over silicon surfaces. The approach used in this work, relies on a combination of surface functionalization with local oxidation nanolithography (LON) and uses electrostatic interactions between PBA-NPs and a charged self-assembled monolayer patterned on specific parts of the silicon surface. By using atomic force microscopy (AFM), magnetometry, infrared spectroscopy (IR) and auger electron spectroscopy (AES) we show that the deposition process does not affect NPs properties. In addition, we present a study on the evolution of AFM nanolithographed SiO2 patterns under sonication.