Motivated by recent experiments on filled polymer thin films, we study the effect of the presence of filler particles on phase separating mixtures. Using a generalized Cahn-Hilliard-Cook model, we show that the preferential wetting of one phase on the filler surface generates transient composition waves in the phase separating blends. The interference of the composition waves from different particles can stabilize the transient patterns, leading to desirable control of the morphology.