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In this work was demonstrated iterative approach of potential fields (gravity and magnetics) inverse problem solution with the aim of correct accounting of sedimentary section. The approach consist of simple model creation and further potential fields forward solution and comparison with the base case and after that model modification. Different iterations of simple model construction were tested on the “ground truth” detailed model with the main features of the West Siberia Palaeozoic deposits. The objective of the research is to minimize effect of sedimentary layers on the gravity and magnetic fields by modeling with geostatistical approach (stochastic simulation with trends) and explain how to use this approach according to real data.