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In most cases 2D inversion is used in commercial projects, because of its effectiveness and great experience. Whereas in the case of 3D inversion is not such a great experience and there are a number of global problems. When switching to 3D inversion of MT data, the requirement for computer technology is significantly increased. In this paper we tried to find the way out of the situation using supercomputer complex «Lomonosov», located in Moscow State University. We will discuss a few examples of three-dimensional inversion of MTS real data and compare it with 2D inversion in terms of time and result interpretation. Each solves a variety of problems: from Ore shallow search to Regional Oil&Gas studies. But all these objects unite a large volume of stations and the presence of three-dimensional distortions. The main task is to compare 2D inversion for those areas with 3D results and shows that the use of three-dimensional inversion with a high-performance computational complex makes it possible to obtain a qualitative result of solving a wide range of problems.