In nano-biotechnology, optoelectronics, and energy research areas, various fabrication methods have been developed for hybrid nanoparticles. A method is developed here for fabricating highly monodisperse three-dimensional hybrid nanoparticles using a unique top-down method based on secondary sputtering lithography. Nanostructures that have been formed on a PEDOT sacrificial layer are transferred from the substrate to an aqueous solution in a process that could be used to successfully disperse a variety of nanoparticle shapes and hybrid nanoparticles. By this method, a fluorescent dye could be encapsulated within the fabricated hybrid nanoparticles for use in bio-sensing and drug-delivery applications