In this Article, two readily available polymers that contain silicon and have different surface tensions, polydimethylsiloxane (PDMS) and polyphenylsilsequioxane (PPSQ), were used to produce polymer blends with polystyrene (PS). Spin-coated thin films of the polymer blends were treated by O-2 reactive-ion etching (RIE). The PS constituent was selectively removed by O-2 RIE, whereas the silicon-containing phase remained because of the high etching resistance of silicon. This selective removal of PS substantially enhanced the contrast of the phase separation morphologies for better scanning electron microscope (SEM) and atomic force microscope (AFM) measurements. We investigated the effects of the silicon-containing constituents, polymer blend composition, concentration of the polymer blend solution, surface tension of the substrate, and the spin-coating speed on the ultimate morphologies of phase separation. The average domain size, ranging from 100 nm to 10 mu m, was tuned through an interplay of these factors. In addition, the polymer blend film was formed on a pure organic layer, through which the aspect ratio of the phase separation morphologies was further amplified by a selective etching process. The formed nanostructures are compatible with existing nanofabrication techniques for pattern transfer onto substrates.