We have characterized the surface morphology and luminescence properties of GaN/AlN/SiC layers of various thicknesses using secondary electron imaging (SET), 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 mum thick AlN buffer layers on commercial 6H-SiC(0001) substrates. The GaN layer thicknesses are 0.5, 1.0, 1.6, and 2.6 mum. A second 1.0 Am thick layer was grown by identical procedures on a 6H-SiC substrate that was first etched in H-2 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 mum layer on the H-etched substrate is as relaxed as the 2.6 mum 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 mum 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 3x10(18) cm(-3) Si do not show these features, suggesting a different microstructure.