An original top-down process involving a bio-template and damage-free neutral beam etching (NBE) has been developed to fabricate a high-quality nanodisk superlattice. The self-assemble ferritin 2D array (iron core diameter: 4.5 nm) acts as uniform etching mask and our developed neutral beam etching eliminates UV photons and high-energy charged particles to achieve a damage-free etching. As a result, we have fabricated a high-quality nanodisk superlattice with a high density (1.4 × 1012 cm-2), uniform size (Si nanodisk diameter: 6.4 nm), and well-ordered arrangement (hexagonal close packing). The Si nanodisk 2D array with SiC interlayer had an extremely high optical absorption coefficient and high carrier transport due to the formation of a wide miniband. This advanced nano-process brings high-efficiency quantum dot (QD) solar cell (SC).