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This study experimentally and theoretically investigated individual GaN-based ultrathin-film micro-light-emitting diodes (μ-uTFLEDs) with photonic crystal (PhC) nanostructures of varying emission aperture sizes from 5 to 100 μm. High-resolution angular-spectra-resolved electroluminescence measurements revealed the guided mode extraction characteristics that dependence on the emission aperture size. Experimental results indicate that the different diffraction vectors of guided modes have varying extraction lengths; therefore, the emission aperture size acts as a gradual guided mode filter. This effect also limits the suitability of GaN PhC μ-uTFLEDs for the optical engine in pico-projectors.