In this work, a new approach for construction of high aspect ratio complex moire superlattice structure with versatile super-periodicity is developed using the moire fringe and secondary sputtering lithography. Wide assortments of high aspect ratio complex superstructures having different features on a 10 nm scaled wall are easily fabricated from simple starting components. More important is the finding of a new microscale phenomenon, consisting in trapping fluids in the centres of the moire hexagonal fringes, as the consequence of the modulation of local hydrophilicty of the pattern. Using this phenomenon, target materials can be selectively and hierarchically confined within the moire superlattice. Hierarchical nanoparticles (QDs) ordering with tunable super-periodicity into selective area of moire superlattice are successfully demonstrated by just solution-casting of toluene based QD solution on patterned surfaces. This observation is expected to elucidate the key morphological factors that govern the physics of liquid behavior on a complex patterned substrate. Accordingly, in the near future, this facile approach for complex superlattice structure could be used as optical substrate for imaging applications and open interesting perspectives in the assembly processes and the handling of the nano-microsized particles.