Creation of new effective bio-artificial structures for tissue engineering and regenerative medicine requires development and implementation of new technological approaches for analysis of micro- and nanostructural features of constructs based on biomaterials and their interaction with cells. A new method of three-dimensional multiparametric analysis of nanostructure, scanning optical probe nanotomography, is presented in this paper, applied to the analysis of cells and biomaterials. Correlative reconstruction of fluorescent marker distributions and nanostructure features allows quantitative evaluation of a number of parameters of three-dimensional nanomorphology of fibroblasts and human hepatocarcinoma cells Hep-G2, adhered to biodegradable scaffolds based on silk fibroin. The developed technology with use of scanning optical probe nanotomography is applicable to investigation of three-dimensional micro- and nanostructure features of biomaterials and cells of different types.