Scanning tunneling microscopy (STM) combined with synchrotron radiation (SR) enabled elemental analysis on solid surfaces at an anometer scale. The principle of analysis is based on the inner-shell excitation of a specific energy level under STM observation. After first demonstrative results on a semiconductor heterointerface (Ge nanoisland on an Si(111) 7 × 7 surface), a second trial of nanoscale elemental analysis by the SR-STM system was accomplished for Cu nanodomains on a Ge(111) 2 × 8 surface. A key to achieve successful results is to effectively increase the signal to noise (S/N) ratio and to extract the element-specific modulation of the tunneling current, which is derived from the inner-shell excitation. An essential point for signal detection with a high S/N ratio is to construct a total system including lock-in amplifier with an optical chopper for high accuracy, and a real-time control system to check the incident-beam condition by observing the beam-induced current profiles. Using these techniques, it has been shown that the SR-STM system provides new possibilities forn anoscale surface analysis.