The stability of bilayer polymer films upon solvent annealing has been investigated with the help of atomic force microscopy (AFM) by taking PMMA [poly(methyl methacrylate), the upper layer] and SAN [poly(styrene-ran-acrylonitrile), the bottom layer] system as an example. Our results indicate that the stability and structure evolution depend crucially on the selectivity of the adopted annealing solvents. In the vapor of acetic acid (HAc, the selective solvent for PMMA), the upper PMMA layer dewets on the stable bottom SAN layer; upon annealing in 1, 2-dichlorobenzene (OBD, the selective solvent for SAN) vapor, the bilayer film remains stable because it is very hard for OBD molecules to penetrate and cross the upper PMMA layer. When dimethylformamide (exhibiting much higher solubility for SAN than PMMA) is used to anneal the specimen, the solvent molecules swell and cross the upper PMMA layer and enrich in the bottom SAN layer. As a result, SAN layer dewets the substrate, producing some SAN droplets while the upper PMMA is “carried” by the movement of SAN. This is the reason for the rupture of the upper film and the formation of “SAN droplets covered by PMMA islands.”