A system for a Fischer-Tropsch synthesis using a three-phase reactor in which a primary filter removes coarse catalyst particles from the product and in which catalyst fines are removed in a secondary filter. Some or all portion of the product wax from the secondary filter can be recycled back to the reactor, either as a back flush medium for the primary filter or directly to the slurry in the reactor, whereby removal of catalyst fines is rendered independent of the rate of wax production.