This work focuses on binary chemical nano-patterning and on aspects related to the self-organization and stability during and after dewetting of thin block-copolymer films on chemically nano-patterned substrates. Regarding surface functionalization with thiols, the exchange of thiols in both liquid and gas phase was first investigated. The aim was to control thiols-assembly on gold and thus to fabricate unscrambled binary chemical nano-patterns. The systems gold-thiols are considered as alternatives to silicon oxide-silanes systems in the chemical nano-patterning processes because of fabrication simplicity reasons. The strategy developed to avoid thiol exchange was used to fabricate unscrambled binary chemical nano-patterns combining a top-down approach, Electron Beam Lithography (EBL), and a bottom-up approach based on the self-assembly of thiols on gold. Than, using the chemically nano-patterned surfaces previously developed, the organization processes of thin block-copolymer films were studied. Thin symmetric and asymmetric diblock copolymer films were deposited on engineered substrates consisting of alternating less and more wettable stripes. By locally tuning the chemical properties of the substrate, the interaction potential between the polymer and the substrate can be manipulated. It was thus possible to force a liquid film to dewet or to self-organize in a variety of configurations through phase preparation, specific interactions, confinement.