Various optical methods areof the most use for contactless investigation of thin semiconductor layers. Frequency dependencies of the refractive index real n' and imaginary n'' parts give an information about the main characteristics of the layer materials: energy gap width, junction density of states, etc. All known methods of thin layer optical characterization imply the total knowledge of substrate material. However, many modern applications deal with thin layer deposited on subtrates of complex and not well-known internal structure. Particularly, in prominent narrow gap semiconductor solar cells, the substrate of semiconductor layer has to be IR transparent, but well DC conducting (conducting glasses, usually metallized). In this work we develop a method to find optical characteristics of semiconductor layers in such a system. We refer our approach to definite case of thin (aprox. 1 micrometer) CdTe films, obtained by means of electrochemical deposition on conducting glass. The surface of the layer was not sufficiently good to hope for relevant ellipsometry, because it hardly allowed to procced reflectance mesaurements at all. Therefore we restricted our considertion with the case of normal incidence of IR light. Making use of the optical matrix formalism leads to a system of two trascendental equations connecting n' and n'' of the semiconductor with measured transmission and reflection coefficients of the whole system and of the substrate alone. The thickness of the film was found from electrochemical data. Unfortunately the equations contain also the phase of the substrate reflection amplitude. In actual situation, this phase is appreciably non zero and makes the system of equations unclosed. We coped with the complicaton by use of another layer of the same semiconductor, but of different thickness, deposited on separate part of the same substrate. Transmission coefficient of this complementary system provide the third equation to exclude the undue phase quantity. (In further studies we suppose to interrupt the electodeposition process for this additional measurements). Numerical solution of the resulting equations gives the frequency dependencies of n' and n'' for the semiconductor material. In conclusion, we propose a new method, case to use, for determination of the optical characteristic of electrodeposited thin semiconductor layers regardless to their subtrates material and structure.