We have developed a fabrication process of Si nanopillars using metal clusters arranged by electron beam (e-beam) lithography. This process forms nanopillars by taking advantage of the fact that metal clusters deposited on Si substrates act as nuclei for self-formation of etch masks during electron cyclotron plasma etching withSF6if the substrate is kept at ∼−135 °C. The clusters are placed on the substrate by an e-beam lift-off technique following a small amount of deposition of metal vapors. Arrays of Si pillars with a regular spacing of 100 nm were actually fabricated using Au, Ag, and Fe clusters. Au clusters yielded 70 nm high pillars with an average diameter of 10 nm and a standard deviation of 1.3 nm, which is exceedingly better than the resolution of the lithography used (∼30 nm). Ag and Fe clusters produced pillars 20 nm in diameter. These results demonstrate that the pillar size is controlled by species of the metal clusters, whereas the position is defined by the e-beam lithography. We have also found that Fe clusters are very durable in the etching process and can produce pillars with a very high aspect ratio: 280 nm high and 20 nm in diameter.