A computer-aided digital microscope for studying microstructures at wavelengths of the second optical harmonic and two-photon luminescence is designed. In contrast to commercial instruments, the microscope is intended to study the image dependence on the angle of incidence, azimuth, and angle of the radiation receipt, as well as the polarization characteristics in organic and inorganic structures. As examples, results of studying nonlinearly optical properties of peptide tubes and microstructures based on zinc oxide are given.