The invention provides methods and systems for separating particles that exhibit different Raman characteristics. The method can include introducing nanoparticles, on which Raman-active molecules are adsorbed, into a photopolymerizable resin and exposing to excite Raman active vibrational modes of the molecules to generate Raman-shifted radiation suitable for polymerizing the resin such that the Raman-shifted radiation causes selective polymerization of a resin surrounding nanoparticles if the nanoparticles provide a Raman enhancement factor greater than a threshold. In addition, methods for electrically isolating nanoparticles, or selectively removing one type of nanoparticles from collections, are disclosed. These methods rely on generation of blue-shifted anti-Stokes photons to selectively expose portions of a photoresist covering the nanoparticles to those photons. Such exposure can cause a change in the exposed portions (e.g., polymerize or increase solubility to a developing agent), which can be employed to achieve isolation of the nanoparticles or their selective removal.