The surface atomic structure of carbon nitride thin films deposited on both Si (100) and highly ordered pyrolytic graphite (HOPG) substrates by microwave plasma chemical vapor deposition technique is studied by scanning tunneling microscopy (STM), STM images of the surface of the films with atomic resolution are obtained. The microstructure of the surface of the film on Si (100) substrate is very complex and composed of various components as confirmed by other techniques. An atomic structure is observed in the complex surface of the film on Si substrate. The unit cell constant of the structure is 4.7 Angstrom along a and b directions with 120 degrees angle between them. This structure is clearly observed in the film deposited on HOPG substrate at a larger scale. The structure is discussed. It is found that the observed structure is will in agreement with the G-C3N4 structure.