The supramolecular layer-by-layer assembly of 3D multicomponent nanostructures of nanoparticles is demonstrated. Nanoimprint lithography (NIL) was used as the patterning tool for making patterned β-cyclodextrin (CD) self-assembled monolayers (SAMs) and for the confinement of nanoparticles on the substrate. A densely packed and multilayered nanoparticle structure was created by alternating assembly steps of complementary guest- (Fc-SiO2, 60 nm) and host-functionalized (CD-Au, 3 nm) nanoparticles. The effects induced by the order of the nanoparticle assembly steps, going from large to small and from small to large nanoparticles by using Fc-SiO2, CD-Au, and CD-SiO2 (350 nm) nanoparticles, were compared. AFM height profiles revealed that the specific supramolecular assembly of nanoparticles was self-limited, i.e. one nanoparticle layer per assembly step, allowing the control over the thickness of the supramolecular hybrid nanostructure by choosing the size of the nanoparticles, irrespective of the core material of the nanoparticles. The roughness of structure, observed by AFM imaging of the top layer, was directly influenced by the size and packing of the underlying nanoparticle layers.