A new scalable approach has been developed for fabricating large-scale pitpatterns with controllable periodicity on Si(001) substrates. The fabricationprocesses start with self-assembling a monolayer of polystyrene (PS) spheres onhydrogenated Si(001) substrates. A novel net-like mask in combination of the Aupattern thermally evaporated in between the PS spheres and the Au-catalyzedSiO2 around them is naturally formed. After selective etching of Si by KOH solution,two-dimensionally ordered pits with a periodicity equal to the diameter of the PS spheresin the range from micrometers to less than 100 nm can be obtained. The shape of the pitscan be modulated by controlling the chemical etching time. Such pit-patterned Sisubstrates facilitate the formation of ordered Si-based nanostructures, such as orderedself-assembled GeSi quantum dots, by deposition of Ge using molecular beamepitaxy.