Development of the Digital Material Representation (DMR) model, based on 3D reconstruction algorithm and serial sectioning, is the main goal of the present paper. Details on the serial sectioning and image processing algorithms are presented first. Serial sectioning is realized on the basis of light microscopy (LM). Then concept of 3D reconstruction and developed algorithms are presented. Two approaches, based on shape coefficients and the flood fill algorithms, are developed to identify corresponding features on subsequent 2D images. Then, the interpolation algorithm to reconstruct 3D volume between 2D images is presented. Finally, obtained 3D model is an input for finite element mesh generation software for subsequent finite element calculations.