We propose a method for reconstructing the thickness variation of one layer of interest inside a multi-layered structure. This reconstruction is based on inverting far-infrared reflection measurements at a few distinct frequencies. This real-time method allows non-destructive evaluation of a multi-layered structure to better control its manufacturing process, whereas other methods have acquisition or computation times that are not compatible with real-time non-destructive evaluation. Two simulated data and one real data based experiments revealed that the method we propose is robust against measurement noise.