A standardless method for the determination of nanometric thicknesses was developed on the basis of the detection of characteristic X rays. The method was developed aiming to the morphological characterization of anodes of lithium-ion batteries, particularly for those based on binder free Si/C binary composites generated by sputtering deposition. Even when the procedure was designed for this particular case of nano-stratified samples consisting of a Si film deposited onto a C layer, which in turn is deposited on a Cu substrate, it is easily extensible to other configurations. To obtain the thickness of the deepest layer it is necessary to know the thickness of the surface layer. For this reason, the calculations involve an iterative strategy based on Monte Carlo simulations. The method was validated in a set of samples whose thicknesses were also determined by Rutherford backscattering spectrometry. In addition, the method was applied to another set of anodes, giving results that matched the expected values.