performance of quantum devices. In this work, we present atomic-level characterization of cross-sections of a Josephson junction and a spiral resonator to assess the quality of critical interfaces. Employing scanning transmission electron microscopy (STEM) combined with energy-dispersive X-ray spectroscopy (EDS) and electron-energy loss spectroscopy (EELS), we identify structural imperfections associated with oxide layer formation and carbon-based contamination, and correlate these imperfections to the pattering and etching steps in the fabrication process and environmental exposure. These results help to understand that TLS imperfections at critical interfaces play a key role in limiting device performance, emphasizing the need for an improved fabrication process.