Dielectrophoresis (DEP) is a phenomenon with directional movement of micro particles due to the DEP force under uneven AC electric field. We utilize polymer surface with microstructures such as µm-scale pit arrays for DEP devices to assemble or concentrate nanoparticles. For micro-structuring of the polymer such as PMMA with thickness of 5-10 µm, we applied proton beam writing (PBW) which is a direct-write lithographic technique for high-aspect ratio microstructures of polymeric materials such as PMMA and epoxy resin. Pit arrays such as 5 x 5 arrays of circular pits with diameter of 5 µm on the 5-10 µm thick PMMA. We were able to demonstrate collection and assembly of gold and Ag nanoparticles (diameter of 100 to 250 nm) on the PMMA pit arrays from the colloidal suspension of the metallic nanoparticles in water. The DEP experiments were performed with the amplitude (10-20 V) and frequency (1-100 kHz) of applied ac voltages with additional dc offset voltage of less than 1V. We also discuss possible application of this technique to the detection of micro and nanoparticles such as plastics, dielectrics and metals in environmental water.