The barrier layer of anodic aluminum oxide (AAO) formed on the silicon substrate was etched with Cl 2 /BCl 3 gas mixtures by a neutral beam and the results were compared with the AAO etched by an ion beam. The etch rate of AAO itself was increased with the increase of BCl 3 in Cl 2 /BCl 3 up to 60% in the gas mixture. And, the etching of AAO itself was related to the Cl radical density in the plasma and the formation of volatile BO x Cl y on the AAO surface for both the neutral beam etching and the ion beam etching. The AAO itself could be etched by both the neutral beam and the ion beam in all Cl 2 /BCl 3 gas mixtures. However, the barrier layer of the AAO located near the bottom of the AAO pore could not be etched using the ion beam etching due to the charging of the nanometer size AAO pore similar to the case of conventional reactive ion etching. Using the neutral beam etching, the barrier layer of AAO pore could be successfully etched with BCl 3 -rich BCl 3 /Cl 2 gas mixtures by removing the barrier layer without charging the AAO pore and by the forming volatile BO x Cl y .Anodization is a technology transforming metal into metal oxide by electrochemical oxidation and it has been actively investigated for the fabrication of nanostructure of various sizes. Especially, the anodic aluminum oxide (AAO) obtained by the anodization of aluminum film is being used as the template and mask for deposition, etching, doping, etc. in the fabrication of various nano devices such as magnetic data storage devices, optoelectronic devices, nano sensors, etc. [1][2][3][4] In general, AAO can be fabricated with various porous nano-hole spacing and diameter in the range of 10-500 and 4-200 nm by controlling anodization voltage and, also by using indentation method, various shapes of AAO such as hexagonal, square, and triangular shaped AAO can be fabricated. 5-7 When the AAO is used as the solid mask, due to the strong bonding of Al 2 O 3 , it shows superior mechanical properties compared to other porous mask materials. 8 Especially, compared to the patterning using electron-beam lithography and block co-polymer, the patterning using AAO is cheaper, more reliable, and easier in controlling the size and shape. 9 In addition, it can be applied to fabricate various two-dimensional lateral superlattice structures by using highly ordered AAO templates. 10 However, due to the stress at the interface between the aluminum and the substrate, the alumina barrier layer is formed at the bottom of the AAO holes during the formation of AAO and it prevents direct physical and electrical contact to the substrate, and it is known to be one of the biggest problems in the formation of AAO. 11,12 To remove the barrier layer, various techniques such as pore widening, cathodic polarization, voltage drop, plasma assisted etching, etc. are investigated. [13][14][15] In the case of pore widening and cathodic polarization, even though the barrier layer can be removed reliably and reproducibily, due to the chemical attack of the sidewall of AAO by OH-formed...