Among other things, the last decade has seen the emergence of two important techno-scientific features, which are the entry of semi-conductor integration technology in the nanometer range, and the explosion of chemical methods allowing to produce or to manipulate functional nano-objects such as macromolecules, proteins, clusters, nanotubes and colloids. It is therefore timely to develop ways to merge these two trends, which would allow significant progresses in these fields where the integration of soft-condensed matter with semi-conductor nanotechnology is of critical importance (biosensors, organic electro- and photo-active devices, molecular engines, etc.). In this context, there is currently an urgent need to succeed in placing organic nano-objects at specific addressable locations on a substrate. For fragile soft organic structures, letting Nature drive functional nano-objects to their docking locations could be a successful route for the fabrication of low cost nano-engineered devices in the near future. In this work, we precisely present a general route allowing to self-assemble macromolecules of varying natures at specific locations defined at the nanometer scale. Assembling instructions are first stored on a substrate, through the combination of electron-beam nanolithography and surface chemical reactions based on reactive silanes. In a subsequent step, the instructions are deciphered by organic molecules brought in contact with the patterned substrate, leading to controlled nanoscale deposition and assembly. The first part of this work consists of the production of surfaces chemically patterned with very high resolution (<<100 nm dimensions), by using gas phase silanation and electron beam lithography. The patterns were imaged and characterized to demonstrate that our technique allows us to obtain chemical templates down to 20-25 nm feature size level, comprising a wide range of chemical functionalities. These patterned surfaces were then used to direct the adsorption or the grafting of various macromolecular compounds, resulting in the formation of macromolecular 3D nanostructures from the 2D binary patterned surfaces. Different interactions were used to control the 3D assembly process, such as electrostatic interactions (layer-by-layer deposition of polyelectrolytes), combined hydrophobic and electrostatic interactions (for the selective adsorption of amphiphilic triblock copolymers), hydrophobic interactions for the local deposition of a protein (antigen 69K from Bordetella pertussis) and valence bond for the grafting of macromolecules at specific locations. For each of these assembling strategies, specific effects resulting from the nanoscale confinement of the macromolecules were evidenced, such as folding of chains of size larger than the 2D directing patches, tuning of antigen orientation, formation of complex block copolymer nanostructures decorating the edges of the 2D patterns, and reduced grafting probability for free radical polymerization on small patches. These results illustrate the rich behavior of macromolecules when approaching nano-patterned surfaces, and suggest that new rules govern macromolecules at this scale.