In case of periodic multilayers, such as for optical filters, X-ray reflectivity (XRR) is mostly used for precise determination of the thickness and density of the layers. However, nonperiodic multilayer systems of more than four to five layers generally cannot be solved by XRR because of the numerous fitting parameters. For a 31-layer system, 96 fitting parameters (which will not converge to a unique solution) have to be matched. Here, secondary ion mass spectroscopy (SIMS) may help by giving reliable start values for the thicknesses. To achieve this, optimum depth resolution and a correction of the different sputter rates of the alternating materials is necessary. Iterative optimization of XRR fit and SIMS layer thicknesses finally yield good correspondence, with a mean deviation of 1.8 nm or 3%. Spectroscopic variable angle ellipsometry has been taken as a third method for the characterization of the layer stack but has yielded slightly larger deviations. Copyright © 2012 John Wiley & Sons, Ltd.