We have characterized the surface morphology and luminescence properties of GaN/AlN/ SiC layers of various thicknesses using secondary electron imaging (SEI), panchromatic room temperature cathodoluminescence (CL), atomic force microscopy (AFM), optical Nomarski microscopy, and room and low temperature photoluminescence (PL). The nominally undoped GaN layers were grown by MOCVD on 0.1 m thick AlN buffer layers on commercial 6H-SiC(0001) substrates. The GaN layer thicknesses are 0.5, 1.0, 1.6, and 2.6 m. A second 1.0 m thick layer was grown by identical procedures on a 6H-SiC substrate that was first etched in H2 to remove scratches and damage due to mechanical polishing. Biaxial compressive lattice mismatch stress is present in all layers and decreases with increasing layer thickness, while PL linewidths decrease. The 1 m layer on the H-etched substrate is as relaxed as the 2.6 m layer on a non H-etched substrate, however. Pronounced surface structures, apparently corresponding to columnar subgrain boundaries, are observed on the samples on non H-etched SiC. Their typical sizes increase from about 3 to 10 m with increasing layer thickness. They are absent in the H-etched sample. These structures are generally nonradiative in CL images, although mottled contrast is also observed inside them. Similar layers doped with 3×1018 cm−3 Si do not show these features, suggesting a different microstructure.