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Polystyrene film of about 50 nm in thickness on silicon wafer was obtained by spin-coating in tetrahydrofuran solution. The film exhibits a rough surface as shown by atomic force microscopy images and ellipsometry data. Furthermore, such surface roughness produced a characteristic lateral correlation peak in an "out-ofplane" scan in the synchrotron grazing incidence ultrasmall angle X-ray scattering pattern. The film was treated with liquids of solvent and non-solvent sequentially, resulting in a process of swelling and precipitation of the polystyrene film. Such a solvent/non-solvent treatment completely changed the original surface structure of the film. Aggregates of polystyrene of different sizes were observed both in atomic force microscopy and synchrotron grazing incidence ultrasmall angle X-ray scattering measurements. The results demonstrate that synchrotron grazing incidence ultrasmall angle X-ray scattering is a unique means to investigate large area micro-structural features of thin films supported on smooth surfaces.