In the early 1960s, scientists achieved the breakthroughs in the fields of solid surfaces and artificial layered structures. The advancement of surface science has been supported by the advent of ultra-high vacuum technologies, newly discovered and established scanning probe microscopy with atomic resolution, as well as some other advanced surface-sensitive spectroscopy and microscopy. On the other hand, it has been well recognized that a number of functions are related to the structures of the interfaces, which are the thin planes connecting different materials, most likely by layering thin films. Despite the scientific significance, so far, research on such buried layers and interfaces has been limited, because the probing depth of almost all existing sophisticated analytical methods is limited to the top surface. The present article describes the recent progress in the nanometer scale analysis of buried layers and interfaces, particularly by using X-rays and neutrons. The methods are essentially promising to non-destructively probe such buried structures in thin films. The latest scientific research has been reviewed, and includes applications to bio-chemical, organic, electronic, magnetic, spintronic, self-organizing and complicated systems as well as buried liquid–liquid and solid–liquid interfaces. Some emerging analytical techniques and instruments, which provide new attractive features such as imaging and real time analysis, are also discussed.