Since the ancient Egyptians had used sand as filter media for water purification, its principle has been inherited through generations and it is still being used now in industries. The sand filter consists of sand literally, and the voids within the sand bed are the pores for filtration. Here we present a filtration principle using nanoparticles, so that the voids between the nanoparticles can be considered as effective pores in nanoscale dimension. Anodic aluminum oxide (AAO) membrane has been used as the working template, and the nanoparticles have been injected and embedded within the pores of the AAO template. Nanoparticles with multiple sizes have been used in order to obtain smaller voids. Moreover, the nanoparticles have been functionalized, or electrically charged, with arginine/phenylalanine (RF) peptide group. In this way, filtration performance for charged particles or molecules, such as methylene blue, has been enhanced. Consequently, this study is expected to provide a new principle for fabrication of nano voids, or nano pores, and for filtration in nanoscale dimension.