AlGaN and its heterojunction alloys are used in some of the most advanced micro- and optoelectronic devices today and rely on precise control of electronic properties in multilayer film structures on a nanometer scale. Deep level defects in these materials and at their interfaces can alter transport, recombination, contact formation, and doping, yet measuring such small structures is a challenge for conventional techniques. Al-rich AlGaN layers can enable many new applications but little is known of their deep level properties. Also, doping of AlGaN with high Al content is difficult and may be restricted by non-intentional impurities (such as oxygen) and their associated deep levels. We have used a near-surface version of cathodoluminescence spectroscopy (CLS), termed low energy electron-excited nanoluminescence (LEEN), to probe the electronic properties of thin HFET films as a function of lateral position and depth. LEEN spectroscopy can provide electronic properties of states that are localized at the surface, buried interface, and near the middle of these nanometer-scale films. For AlGaN/GaN structures, correlations have been made between deep level defects and the sheet charge density, AlGaN/GaN intermixing, surface roughness, and Ga/N ratio. We have also used LEEN with secondary ion mass spectrometry (SIMS) to correlate deep levels across the AlGaN alloy series with chemical impurities and spatial location at surfaces, interfaces, and in the bulk. Al-rich AlGaN exhibits deep level optical emissions that correlate with O and C impurities. Temperature-dependent CL of the Si-doped films reveal donor energy increases but activation energy decreases with Al content. Coupled with the appearance of an O deep level at mid-gap at highest Al concentrations, these changes can be seen to compensate the intentional Si doping. These results demonstrate how spatially-resolved CL combined with SIMS can provide new understanding of macroscopic III-nitride properties.