Si nanodot arrays were fabricated by high density plasma etching of tantalum oxide pillar arrays and Si thin films. Tantalum oxide pillar arrays self-assembled during anodic aluminum oxide process were employed as etching masks. The etch rates of tantalum oxide and Si films and etch selectivity of Si to tantalum oxide mask were investigated as a function of the etching gas, coil rf power, dc bias to suseptor. The etch profiles of Si nanodot arrays were observed by filed emission scanning electron microscopy. Finally, the formation of Si nanodot arrays was successfully achieved at the optimized etch conditions.