Cellulose acetate fibers with magnetic properties have recently attracted much attention because of their potential novel applications in biomedicine such as for cell and protein separations, magnetic resonance imaging contrast agents, and magnetic filters. In this work, as synthesized yttrium iron garnet and gadolinium substituted yttrium iron garnet nanoparticles have been used to generate magnetic filter paper. Garnet nanoparticles dispersed in cellulose acetate polymer solutions were electrospun as free-standing nonwoven fiber mats as well as on cellulose filter paper substrates resulting in magnetic filter papers. The magnetic fibers were characterized by scanning electron microscopy (SEM), transmission electron microscopy (TEM), powder X-ray diffraction (PXRD), and superconducting quantum interference device (SQUID) magnetic property measurements. The resulting magnetic polymer nanocomposites can be easily picked up by an external magnet from a liquid medium. Fluorescein isothiocyanate (FITC) labeled bovine serum albumin (BSA) was separated from solution by using the magnetic filter paper.