The column for cryogenic (C-13) isotope separation is studied in this article, using equipment belonging to the National Institute of Research and Development for Isotopes and Molecular Technologies (INCDTIM), Cluj Napoca. The complete dynamics of the column is represented by nonlinear partial differential equations, the so called Cohen's equations, which depend on the time as well as the spatial coordinates, but which are not appropriate for online applications and control needs. The proposed solution is to identify fractional order model from frequency response or from time response of the system. The model is validated by simulation, highlighting the performance of fractional order models in comparison with the integer model and experimental data of the column.