Highly ordered silicon nanorod (SiNR) arrays with controllable geometry are fabricated via nanosphere lithography and metal-assisted chemical etching. It is demonstrated that the key to achieving a high-quality metal mask is to construct a non-close-packed template that can be removed with negligible damage to the mask. Hydrophobicity of SiNR arrays of different geometries is also studied. It is shown that the nanorod structures are effectively quasi-hydrophobic with a contact angle as high as 142 • , which would be useful in self-cleaning nanorod-based device applications.