In this article, we show the mechanism for the observation of subsurface structures by scanning tunneling microscopy (STM), which has not been explained by common sense of STM. It is clarified that the properties of electrons as waves, especially, qualitative difference between nano-scale and atomic-scale waves and 3-dimensional tunneling phenomenon in STM play important roles in observing subsurface structures by STM. As examples, we discuss moire patterns in lattice-mismatched systems and the oscillations observed around bulk impurities in semiconductors.