The research of thin films of various materials on nano- and microlevel is undoubtedly topical. Three-dimensional images of thin films can significantly increase the level of the received results. Intellectual computer support of researches assumes the existence or creation of mathematical and the software that implements the experimental program. Such support can most effectively be realized with the help of an information and expert system, based on a holographic electron microscope. In this work we presented an information and expert system for solving this problem. When creating instrumental, hardware and software tools for non-destructive research of the 3D structure of objects, we proceeded from the assumption that the most complete information about the object of research can be obtained only with a comprehensive approach to the analysis of the structure of the object using complementary techniques that allow obtaining data 3D image.