We developed a fabrication process of regular arrays of Si nanopillars using self-formation of etching masks with metal clusters as formation nuclei. When Si substrates deposited with metal clusters are subjected to electron cyclotron plasma etching with SF6 at around -130 °C, reaction products in the plasma, SxFy, condense preferentially at the clusters, leading to the self-formation of nanoscale etching masks. As a result, Si pillars, about 10 nm in diameter and 100 nm tall, are formed with remarkably narrow size-distributions when Au clusters of 1-3 nm diameter are used. This method can be easily combined with electron beam lithography technique, which enables us to define pillar positions. Using this process, we have fabricated 2 dimensional photonic crystals (square and triangular lattices of Si nanopillars) with photonic band gaps in the visible and near infrared regions. We measured reflection spectra of the photonic crystals and observed polarization-dependent reflection bands in the wavelength range consistent with theoretical calculations.