Adam Green

Ultrafiltration membranes are a great suggestion but the dead end / direct flow filters can block. You should take a look at lab scale tangential flow filtration (TFF) / crossflow filtration devices as these don't block and can do volumes from 50ml to 5L. 

The Millipore Amicons just use a Regenerated Cellulose based membrane, you could try the Sartorius PES based membrane filters. You could the further passivate the ultrafilter by washing with a buffer like Tween, Triton, PEGS to bind to the non-specific binding points in the membrane.