Fracture networks are abundant in subsurface applications (e.g., geothermal energy production, CO2 sequestration). Fractured reservoirs often have a very complex structure, making modeling flow and transport in such networks slow and unstable. Consequently, this limits our ability to perform uncertainty quantification and increases development costs and environmental risks. This study provides an advanced methodology for simulation based on Discrete Fracture Model (DFM) approach. The preprocessing framework results in a fully conformal, uniformly distributed grid for realistic 2D fracture networks at a required level of precision. The simplified geometry and topology of the resulting network are compared with input (i.e., unchanged) data to evaluate the preprocessing influence. The resulting mesh-related parameters, such as volume distributions and orthogonality of control volume connections, are analyzed. Furthermore, changes in fluid-flow response related to preprocessing are evaluated using a high-enthalpy two-phase flow geothermal simulator. The simplified topology directly improves meshing results and, consequently, the accuracy and efficiency of numerical simulation. The main novelty of this work is the introduction of an automatic preprocessing framework allowing us to simplify the fracture network down to required level of complexity and addition of a fracture aperture correction capable of handling heterogeneous aperture distributions, low connectivity fracture networks, and sealing fractures. The graph-based framework is fully open-source and explicitly resolves small-angle intersections within the fracture network. A rigorous analysis of changes in the static and dynamic impact of the preprocessing algorithm demonstrates that explicit fracture representation can be computationally efficient, enabling their use in large-scale uncertainty quantification studies.