A combined process of electrochemical formation of self-assembled porous anodic alumina thin films on a Si substrate and Si etching through the pores was used to fabricate ideally ordered nanostructures on the silicon surface with a long-range, two-dimensional arrangement in a hexagonal close-packed lattice. Pore arrangement in the alumina film was achieved without any pre-patterning of the film surface before anodization. Perfect pattern transfer was achieved by an initial dry etching step, followed by wet or electrochemical etching of Si at the pore bottoms. Anisotropic wet etching using tetramethyl ammonium hydroxide (TMAH) solution resulted in pits in the form of inverted pyramids, while electrochemical etching using a hydrofluoric acid (HF) solution resulted in concave nanopits in the form of semi-spheres. Nanopatterns with lateral size in the range 12-200 nm, depth in the range 50-300 nm and periodicity in the range 30-200 nm were achieved either on large Si areas or on pre-selected confined areas on the Si substrate. The pore size and periodicity were tuned by changing the electrolyte for porous anodic alumina formation and the alumina pore widening time. This parallel large-area nanopatterning technique shows significant potential for use in Si technology and devices.