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A microfabricated magnetic sifter has been designed and fabricated for applications in biological sample preparation. The device enables high-throughput, high-gradient magnetic separation of magnetic nanoparticles by utilizing parallel fluid flow through a dense array (~500 /mm2 ) of micropatterned slots in a magnetically soft membrane. Finite element models have been carried out to map the magnetic field and magnetic field gradients of two variations of slot geometry resulting in two distinct capture behaviors. Experimental separations have been conducted using 20 nm diameter iron oxide nanoparticles with streptavidin functionalized surfaces. Inspection of the sifter with a scanning electron microscope revealed dense aggregates of nanoparticles captured at the regions of high magnetic field gradients calculated by the finite element models. Capture efficiencies ranging from 88.8%-100% were measured for a single pass through the sifter, and elution efficiencies ranging from 50%-70.5% were measured for a single elution step.