The controlled fabrication of submicrometer phase-separated morphologies of semiconducting organic materials is attracting considerable interest, for example, in emerging thin-film optoelectronic device applications. For thin films of spin-coated blends of PCBM ([6,6]-phenyl-C-61-butyric acid methyl ester) and cationic cyanine dyes, we used atomic force microscopy scans to infer the structure formation mechanism: The solutions separate into transient bilayers, which further spinodally destabilize because of long-range molecular interactions. A thin layer ruptures earlier than a thick layer, and the earlier instability determines the morphology. Consequently, the resulting morphology type mainly depends on the ratio of the layer thicknesses, whereas the periodicity of structures is determined by the absolute film thickness. These findings allow control of the feature sizes, and nodular domains with diameters well below 50 nm were produced. Films prepared with dyes possessing a mobile counterion were always unstable. To rationalize the findings, we developed a thermodynamic model showing that electrostatic forces induced by the mobile counterions act as destabilizing pressure.