In this paper, we present a new low voltage biochip for micro and nanoparticle separation. The proposed system is designed to detect the concentration of particles after being separated through reconfigurable DEP-based electrode architecture. The described system in this work is focusing on the particle frequency dependent separation. Experimental results in artificial cerebrospinal fluid (ACSF) show that each particle has its own crossover frequency. Thus based on the crossover frequency, particles are attracted to the electrode's surface, while others are pushed away. Five different particles are tested with different diameters in the range of 500 nm to 4 µm. All separation process is controlled by a CMOS chip fabricated using 0.18 µm technology from TSMC and powered with 3.3 V. Efficient particle separation is observed with low voltage, below 3.3V unlike other techniques in the range of kV. The proposed platform includes an advanced PDMS based assembly technique for fast testing and prototyping in addition to reconfigurable electrode architecture.