The fabrication of 3D nanostructures, which have tunable, sub-100 nm dimensions in all three directions, is a key issue of nanotechnology. Here we describe the integration of top-down nanoimprint lithography (NIL) and bottom-up layer-by-layer (LBL) assembly for the preparation of 3D hybrid nanostructures. NIL provided down to sub-100 nm poly(methylmethacrylate) (PMMA) structures. These were employed to fabricate patterned self-assembled monolayers of cyclodextrin (CD) host molecules on silicon oxide . The consecutive LBL assembly with adamantyl guest-functionalized dendrimers and CD-modified gold nanoparticles resulted in patterned multilayer structures with thicknesses of 3-30 nm. The x,y control by NIL and the z control by LBL assembly ultimately allowed the fabrication of circular structures with a radius of 25 nm and a thickness of 20 nm. The integration of the two methods has thus yielded a versatile 3D nanofabrication methodology comprising of 10-40 process steps.