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In this report, we proposed a prototype of microchip level SERS (surface enhanced Raman spectroscopy) substrate prepared by applying a DEP force to enforce local aggregation of silver nanoparticles at a target location, as a new sensing system for real time and in-situ detections. For the test, pyrazine as a test molecule was adsorbed on the silver nanoparticles having a diameter of 20 nm, and then analyzed in aggregate. Especially, a small amount of sample was applied on castellated electrodes device, and SERS analysis was performed on the chip. The castellated microelectrodes device was designed and fabricated to have very short gaps of between 0.6 μm and 2 μm to exert a sufficient DEP force (sub-pN) toward the silver nanoparticles. A methodology is presented to locally aggregate the low-density silver colloidal nanoparticles into silver nanoparticles-based SERS substrate.