We report on the characterization of GaN/AlGaN high electron mobility transistor (HEMT) structures grown by molecular beam epitaxy and metal-organic chemical vapor deposition techniques on semi-insulating SiC substrates. We have exploited the surface and interface sensitivity of the grazing incidence x-ray reflectivity (GIXA) technique and combined it with atomic force microscopy (AFM) and x-ray diffraction to obtain an accurate evaluation of the surfaces and channel interfaces for HEMT structures. The presence of smooth interfaces is responsible for the observation of intensity oscillation in GIXA, which is well correlated to step flow observation in AFM images of the surface. While GIXA provides a macroscopic average of the surface and interface roughness, the AFM provides us with a microscopic view of surface roughness. Further, the x-ray diffraction results have been combined with reflectivity data to evaluate the layer thickness and Al mole fraction in the AlGaN layer. The capacitance-voltage (C-V) technique is used to determine the electrical properties of two-dimensional electron gas depth and hence the AlGaN layer thickness. The C-V results are in good agreement with the x-ray data.