Conventional DNA separation procedures involve large sizes, high voltages and are unfit for large molecules. Proposed set-up constitutes two fold separation techniques, porous filter for fractionating strands on size and final run through microchannels (agarose, buffer solution) viscous enough for DNA electrophoresis. For arriving at the final set-up all the physical contradictions like voltage, viscosity of the fluid, length of the channel were analyzed.The physical set up consists around 20 microchannels (varying diameters) positioned at 500um (centre-to-centre spacing) assembling entire device within 1cm. Polymerase Chain Reaction (PCR) treated DNA assays, are fed to microchannel entrances. Mixture of DNA strands are then passed through magnetic filters. Filtering property of the filters is adjusted by regulating corresponding magnetic field strengths. Smallest strands pass through small pored filter, owing to high velocity (in electrophoresis), thus categorization being done. Proposal replaces conventional apparatus by miniaturized equipment, in ideal case disposable. Miniaturization reduced voltages requirement, solving high-voltage handling problems. Proposed apparatus can fractionate large (>200kbp) molecules and even organic molecules.