We present a multi-stage, multi-frequency carbon dielectrophoresis (CarbonDEP) device for high throughput filtering and separation applications in the health care and biotechnology fields. CarbonDEP refers to the use of carbon surfaces to induce Dielectrophoresis (DEP). Up to X high aspect ratio carbon electrode arrays are sequentially embedded in a microfluidic channel and excited with different optimized signals, provided by a custom engineered multi-channel, programmable signal generator, in their frequency and magnitude to obtain X dielectrophoresis-active filters, or a super filter with X stages. Particle separation is achieved by sequentially releasing and collecting the particles previously trapped at different arrays. We demonstrate the feasibility of a 2-stage system by separating 3 particle populations. We also discuss how such system is best applied when working with specific sample types.