During the development of uranium deposits that use in-situ leaching extraction method, mineralogical and lithological structure of sub terrain media remains unknown and is limited to the data along the wells. In order to optimize the development process, the scheme of geotechnological polygon should be positioned by taking into account lithological and mineralogical characteristics of the deposit. Given article describes results of modeling of lithological and mineralogical structure of uranium deposit by using inverse distance weighting and kriging methods, that are widely used in oil and gas industry. These algorithms are part of interpolation module of geotechnological simulator software that was developed and integrated to the Institute of High Technology (KazAtomProm, Kazakhstan) for the purpose of optimization of the processes of uranium deposits development and production. The results show that these two methods can be practically used in Kazakhstan’s uranium industry and the comparison show that values of uranium concentration, permeability coefficient and lithological rock type provided by kriging algorithm are more reliable and closer as compared with other method when applied on the uranium deposit. The developed software that focuses on uranium deposits would eventually reduce costs of Kazakhstan’s mines related to purchasing of costly CAD systems and drilling expensive exploration wells.