We introduce a theoretical method for simultaneous measurement of refractive index and thickness of multilayer systems using Fourier domain optical coherence tomography (FD-OCT) without any auxiliary arrangement. The input data to the formalism are the FD-OCT measured optical path lengths (OPLs) and properly selected spectral components of FD-OCT interference spectrum. The outputs of the formalism can be affected significantly by uncertainty in measuring the OPLs. An optimization method is introduced to deal with the relatively large amount of uncertainty in measured OPLs and enhance the final results. Simulation result shows that by using the optimization method, indices can be extracted with the absolute error for transparent biological samples having indices .