Layer-by-layer self-assembly is a key enabling technique in nanotechnology. It is very crucial to pattern the self-assembled thin films for the realization of nano/microelectronics devices or NEMS (Nano Electro Mechanical Systems). Two approaches to generate spatially separated patterns comprised of organic or inorganic nanoparticles are demonstrated. The processes are based on the lithographic patterning of the nanoparticle-based thin films which are layer-by-layer assembled. This opens to industrial applications of popular layer-by-layer method to produce multilayers for polymers, nanoparticles and protein organized in nanometer scale. These two methods are referred to by us as "lift-off" and "metal mask", respectively. Sharp and clear patterns are created with both methods and images are recorded by scanning electron microscope. Their advantages and disadvantages are discussed and potential usage in 3-D nanostructure fabrication is investigated. In addition, temperature-dependent experiment has first been carried out to make this techniques more practical for micro/naoelectronics or NEMS devices.