In the last past years, many promising applications of nanoparticles in quantum electronics such as nanocrystal memories, chemical sensors or nanodevices based on single electron tunneling and Coulomb blockade effects have attracted much attention. Nanoparticles synthetised by a chemical way are good candidates for those applications thanks to the huge diversity of materials usable and the possible chemical functionalisation of their surface. To make the active part of a nanodevice, those particles must be assembled in a controlled way on the desired areas. The most efficient way, compatible with microelectronics fabrication processes, seems to be a combination of bottom-up and top-down technologies. To take up this challenge, we propose to deposit the nanoparticles on a surface locally functionalised in order to increase the adhesion of nanoparticules on those areas. The ligands used to functionalise and to stabilise the nanoparticles must be terminated by a chemical function complementary to the one present on the substrate surface. Since the ligands have a strong influence on the electronics properties of the nanoparticules, we decided to work on a reference system : gold nanoparticles covered by alkyl-thiol ligands. These one are made by decomposition of an organometallic precursor in toluene with the presence of oleylamine to stabilise the nanoparticles. Oleyamine ligands are exchanged with dodecanethiol, the solution is then purified and nanoparticles are redissolved to give dodecanethiol protected gold nanoparticles in solution in chloroform. In this work, we propose to use Van Der Waals interactions to assemble these particles on specific hydrophobic patterns defined on SiO2/Si substrates by stencil lithography and atmospheric pressure chemical vapour deposition of silane. First, micro and nano-windows are opened in a Poly(Methyl Methacrylate) (PMMA) resist layer by reactive ion etching through a stencil mask. This stencil lithography process allows to pattern all kinds of organic resists which may not be photosensitive. Then, a self-assembled monolayer of octadecyltrimethoxysilane (OTMS) is deposited by atmospheric pressure chemical vapour deposition. The PMMA is finally lift-off leaving the bare hydrophilic SiO2 surface and the OMTS hydrophobic patterns.