The present work demonstrates nanoscale etching of silicon with standard aqueous fluoride etchants running through the hydrophilic domains of a vertically aligned copolymer template. The delivery of etchants was unprecedentedly achieved by an etchant-solution-saturated agarose gel stamp, a technique we call print diffusion etching. Three-dimensional nanoprotrusion features with controllable shapes and sizes (about 20 nm) were formed. To prove that the block copolymers serve to direct the silicon surface morphology by controlling the spatial location of the reaction as well as concentration of reagents, the same etching steps both on silicon and PS-b-PEO (polystyrene-block-polyethyleneoxide) templates were carried out for comparison. The mechanism of the nanoprotrusion formation was elucidated, and the morphology evolution vs. etching time studied.