A complex of interrelated methods and means of analysis, clustering, segmentation and classification of objects on images obtained by sensors of different physical nature (with the help of modern methods of radiography, computer and magnetic resonance imaging) is proposed, which will allow modeling the optimal form of a bone substitute with functional properties by CAD/CAM/CAE design methods, depending on the anatomical data, the nature and localization of the cavity bone defect, its size, load conditions and patterns of bone tissue neoplasm. Methods for making multi-criteria decisions have been developed, which will allow for their implementation for a wide range of optimization tasks of researching the correlation of the shape and size of porosity with indicators of the stress-deformed state of bone substitutes in order to maintain the structural integrity of the biomaterial in the process of regeneration of hard tissue.