Article investigates the change in the geophysical properties of rocks in the process of extracting the rock sample from great depths. Evaluation of changes in effective elastic properties, porosity and permeability of rock samples during extraction was carried out by means of finite element modeling. Assessment of the critical dimensions and orientation of internal defects, leading to the destruction of the rock samples during extraction from great depths, has been made based on the methods of linear destruction mechanics. Approach that makes it possible to calculate the change in the mechanical properties, porosity and fracturing of reservoir rocks in the process of extracting the rock sample from depths to the surface is proposed. Use of refined data on the mechanical properties of recoverable rock samples makes it possible to increase the accuracy of digital geological models required for geological exploration, determination of reservoir properties and oil and gas saturation of a field, and development of oil and gas deposits. Application of such models is especially relevant at all stages of the fields development with hard-to-recover reserves.