One of the main objectives of geoelectric prospecting is mapping of the consolidated low-conductivity basement geometry. To resolve the issue, it will be equally important to delineate local structures at the bottom of the sedimentary complex and to estimate the misinterpretation of results due to the presence of areas with nonuniform conductivity in the stratified geologic cross section. Another relevant objective of EM sounding is to resolve the problem of delineation of anticlinal oil and gas traps. The horizontally layered model with a local inclusion of 3D abnormal areas is certain to fit for the above-mentioned objectives. The study is concerned with the technique of nonstationary EM sounding. When applied for the solution of structural problems, this technique considers the uniform distribution of fields within relatively large volume units of the space explored. Consequently, it results in the more efficient application of the perturbation technique (Born approximation) for the solution of the forward electrodynamics problem. The study presents the findings of 3D tomographic inversion with the use of synthetic and physical modeling data. They definitely allow us to acknowledge that the proposed mathematical apparatus for 3D inversion based on Born linearization of the forward problem has proved to be quite applicable.