It depends on your reaction, but these are likely very fine precipitates. Just about any filter: filter paper, glass wool, whatever is going to clog sooner or later.
If you have access to a centrifuge, you can make the best pellet possible, and decant.
I have to assume, you have some water-soluble synthesized organic in the aqueous phase, and you can't spare even a drop of loss? Because that just comes with the territory of these sorts of precipitates, you have to accept some loss. There are other things you can do, if you think about what you really need.