We present a new approach for detecting interlayers in gallium-nitride (GaN) semiconductor structures bonded on single or polycrystalline diamond. GaN-on-diamond is advantageous because it integrates and effective heat spreader into GaN devices, which is important for high power density operation. However, analyzing GaN/diamond interlayers can be difficult because of nonuniformity as well as atomic-scale roughness across the wafer. In this work, we studied GaN/diamond samples using Raman spectroscopy and employed adaptive principal component analysis (PCA) to explore silicon interlayer properties. For each GaN sample bonded to diamond, the presence of a silicon interlayer was confirmed using high resolution scanning transmission electron microscope (HR-STEM) and electron energy loss spectroscopy (EELS). For comparison, we collected Raman spectroscopic data at 25 degrees C (5 different locations across the wafer, 10 microns apart in each direction) using 10 Raman spectrum acquisitions at each location in the 300-800 /cm range. Raman spectra only show three distinct vibrational modes at similar to 482 /cm, similar to 568 /cm and similar to 735 /cm, associated with the external lamp, GaN E-2 (high) and A(1) (LO) phonon modes. When spectra were analyzed using adaptive PCA, results reveal buried information in the baseline pertinent to the interlayer, including the similar to 520 /cm (silicon) phonon mode as well as similar to 360 /cm, and similar to 760 /cm modes, owing to nanoscale nonuniformities. Improved analysis of ultra-thin silicon interlayers in GaN/diamond opens up new opportunities to examine the impact of growth/post-growth steps, carrier density, and structure for modeling thermal boundary conductance.