Its typically not advisable to remove all of the bio-balls from an established tank at once -- since this is where your anaerobic bacteria are mostly living, removing the bio-balls at once will typically reduce your nitrogen-reducing abilities greatly, potentially causing problems. The recommendation I typically see is remove 1/4-1/5 of the bio-balls at a time, while replacing with live rock if this is your ultimate goal. Alton's suggestion would work very well -- a 'fuge works best when the water is slowly 'dredged' through it -- more contact time for all the bacterium/microfauna involved.

-Corruption