Formation of the ordered array of nanoholes on Si was investigated by the use of the self-organized porous alumina nanoholes array etching mask that is directly formed on the Si substrate by sputtering and subsequent anodic oxidation. Reactive ion etching using chlorine plasma against a porous alumina/thin-SiO2(10 nm)/Si substrate with a high self-bias of rf plasma was revealed to be very effective for pattern transfer to Si. After pattern transference a significant reduction of hole size was observed. In fact, the initial porous alumina hole size of 45 nm is reduced to 13 nm Si holes when the higher aspect ratio of porous alumina nanoholes mask is used. The etching characteristics strongly suggest that not only chemical etching but sputtering occurred, and that redeposition of nonvolatile materials in nanoholes plays an essential role in the reduction of the hole size.