We consider methods of computer-aided quantitative analysis of structure of composite materials that are biologically active, that is, biological objects of natural generation, and materials that are created by using the method of immobilization of biological structures on porous bases. For the last case, we present the computer-aided quantitative analysis of parameters of structure of bases for biologically active composite materials containing biologically active components. It is shown that the quantitative characteristics of structural elements of bases should be taking into consideration for each stage of spatial structure of biologically active composites both at a technological stage of their forming and in course of their functioning. It is emphasizing that the structure compound from a polymer and a living matter is a particularly complex bio-composite material. We consider main tendencies in technology of visualization and quantitative analysis of structure of biologically active composite materials. We discuss examples of application of quantitative structural characteristics for prediction of functional properties of biological objects (biological polymers, cells, tissues, organs, organisms). We present the outlook for development of molecular and cell micro-mechanics.