In this paper we investigate the validity of the optically thin assumption in the transition region of the late-type star AU Mic. We use Far-Ultraviolet Spectroscopic Explorer (FUSE) observations of the C Iii multiplet and O Vi resonance lines, hence yielding information at two different levels within the atmosphere. Significant deviations from the optically thin fluxes are found for C Iii in both quiescent and flare spectra, where only 60% of the flux is actually observed. This could explain the apparent deviation of C Iii observed in emission measure distributions. We utilize escape probabilities for both homogeneous and inhomogeneous geometries and calculate optical depths as high as 10 for the C Iii 1175.71 Åcomponent of the multiplet. Using a lower limit to the electron density (1011 cm-3) we derive an effective thickness of <100 km for the scattering layer. The emission originates from very small and compact regions, consistent with a filling factor of 10-5 derived for the flare plasma.