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We use near-field scanning optical microscopy (NSOM) to probe the local optical and morphological properties in annealed, vacuum-deposited Alq3 films (10−480-nm thick) with 10−100-nm resolution. We use concurrent shear force microscopy (an analogue to atomic force microscopy, AFM) to correlate the morphology of different regions to intensity variations in our fluorescence images as well as variations in the localized fluorescence spectra. We have observed nanoscale effects of annealing temperature on film morphology and fluorescence emission. Our studies show that Alq3 films annealed below the glass transition temperature of Alq3 (T < Tg = 172 °C) were very similar to unannealed films, except in very thin films (<50 nm). Films annealed above Tg (T = 200 °C) for the same amount of time exhibit increased surface morphology and decreased fluorescence. In sufficiently thick films (≈500 nm) annealed at 200 °C, we observe the formation of microcrystalline domains.