We have developed a single-step, high-throughput methodology to selectively confine sub-micrometer particles of a specific size into sequentially inscribed nanovoid patterns by utilizing electrostatic and entropic particle–void interactions in an ionic solution. The nanovoid patterns can be rendered positively charged by coating with an aluminum oxide layer, which can then localize negatively charged particles of a specific size into ordered arrays defined by the nanovoid topography. On the basis of the Poisson–Boltzmann model, the size-selective localization of particles in the voids is directed by the interplay between particle–nanovoid geometry, electrostatic interactions, and ionic entropy change induced by charge regulation in the electrical double layer overlapping region. The underlying principle and developed method could potentially be extended to size-selective trapping, separation, and patterning of many other objects including biological structures.