Total wet nanopatterning on silicon wafer surface by using liquid-crystalline (LC) integrated amphiphilic block copolymer (BC) masks with perpendicularly aligned poly(ethylene oxide) (PEO) cylindrical domains as molecule-transport channels is demonstrated. This smart BC mask enables us to fabricate hexagonally arranged nanohole arrays, by nanopatterning of silicon wafer surfaces, with tunable periodicity in a range of 16–40 nm and precise transcription with an accuracy of a few nanometers. Blending poly(ethylene glycol) monomethyl ether into the PEO cylinders to be nanochannels is a key trick to induce effective transportation of both etching reagents and products in the successful wet nanopatterning. The BC lithography with our smart BC masks and wet etching processes may be evaluated as a low-cost and mass-productive wet nanopatterning of silicon wafers, and may be applied to wide variety of substrates such as metals, semiconductors, glasses, and polymers by choosing appropriate etching reagents.