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Angle resolved X-ray photoelectron spectroscopy (ARXPS) and secondary ion mass spectrometry (SIMS) investigations have been carried out to characterize the GaN cap layer in AlGaN/GaN HEMT structure. The paper discusses the qualitative (presence or absence of a cap layer) and quantitative (cap layer thickness) characterization of cap layer in HEMT structure non-destructively using ARXPS measurements in conjunction with the theoretical modeling. Further the relative sensitive factor (RSF=σGaσAl) for Ga to Al ratio was estimated to be 0.963 and was used in the quantification of GaN cap layer thickness. Our results show that Al/Ga intensity ratio varies with the emission angle in the presence of GaN cap layer and otherwise remains constant. Also, the modeling of this intensity ratio gives its thickness. The finding of ARXPS was also substantiated by SIMS depth profiling studies.