Centrifugation may be an option, though ultracentrifugation may be required for such small beads. Another option could be to use a centrifugal filter unit with a very high molecular weight cutoff such that, the enzyme will pass through the filter, and you can collect the beads in the filter unit. For concentrating viruses (also particles with ~ 100 nm size) from solution, PEG precipitation is often used, though I'm not sure how efficient this will be at completely removing the enzyme.