The MEСOS-C2 multifunction scanning microscope-analyzer is intended for automation and informatization of medical, research, veterinary and production techniques of biomaterial analyses. The family of MECOS-C2 models uses a group of hardware platforms with full automation and productivity range from manual digital microscope to autonomous robot. The MECOS-C2 software implements on any platform a group of specialized scanners, search engines and analyzers for different types of specimens. Scanners can produce representative digital lookalikes of specimens, search engines and analyzers can search and analyze investigation objects. MECOS-C2 provides tools of remote access and telemedicine advice to digital lookalikes of specimens.