The paper presents some results of the development of a digital permanently operating structural and geological model (implemented at the Autonomous Institution of the Khanty-Mansiysk Autonomous District–Yugra V.I. Shpilman Research and Analytical Center for the Rational Use of the Subsoil) for the area of central West Siberia and important aspects that need to be considered in implementation practice. The methodological challenges of the variational-grid mapping method and its application include problems such as finding an optimal computational grid and using heterogeneous input information for mapping key seismic horizons. An effective method is considered for using seismic data with uncorrected misties in geological mapping based on corrections for derivatives of the desired function along the seismic profile direction (i.e., seismic surface shape). Special attention is paid to a priori information when mapping stratigraphic boundaries with poorly correlated seismic sections. The conformal thickness model linking geometry of the mapped surface with the structural framework of the two reference boundaries has been tested on the construction of regional structural and geological models for the Jurassic interval of the cross section of West Siberia. The model modification can also be applied to mapping clinoform formations. Given the scale and nontrivial tasks of regional mapping, the issues related to setting up the computing workflow are considered in detail: algorithmization, programming protocols, and automation. In the light of the accentuated relevance of the development of specialized software, the GST (Geo-Spline Technology) software product is considered, with the digital structural framework of the region implemented therein. This resulted in a permanently operating model, since the hierarchical object-oriented approach implemented in GST ensures a complete protocol that integrates computational procedures and data flows, as well as automation of model recalculation. The structural framework serves as the basis for mapping physical properties and parameters, assessment of the region resource potential, and r study of other aspects. The proposed model being not conclusive, it offers rich opportunities for revision and refinement as to the area size (geological model domain), level of detail, database enlargement, thereby determining the directions of further development of the digital structural framework.