jats:pDuring annealing, the morphologies of thin InGaN epilayers have been observed to change from a terraced structure to a network of interlinking InGaN strips separated by troughs. This change in morphology may contribute to high efficiencies in some GaN-based light emitting diodes (LEDs) if the InGaN is exposed to elevated temperatures without a protective GaN capping layer. Here, we investigate the changes in morphology which occur when InGaN epilayers are annealed at their growth temperature under NH3, N2, and a small H2 flux. We observe that while the layers initially roughen, more extended anneals lead to the surface becoming smooth and terraced once again. Power spectral density analysis of atomic force microscopy data is used to show that the dominant mechanism for roughening is loss of material from pre-existing pits, while the dominant smoothening mechanism is surface diffusion. This mechanistic analysis may be relevant to the growth of InGaN quantum wells in LED structures.</jats:p>