This article presents an inverse analysis method based on an instrumented indention to extract materials properties from multilayer material systems. In this case, a 12-layers system comprising of two alternate materials is considered. Each layer is 1 μm thick. The material properties selected for the layers are within the range of common commercial aluminium alloys. The yield stress and strain hardening exponent of the two layers were identified based on a power law type equation to define the stress-strain relationship. A 2D axis-symmetric indenter having 70.3 half angle was used, which is representative of a Berkovich or a Vickers indenter. The use of finite element analyses was substituted with a fast and equally accurate approach for the iterative optimization procedure. Thus, the computation time was considerably reduced. The robustness is tested using pseudo-experimental results, in terms of indentation curve and imprint on the material, with added random noises of 2.5%, 5.0%, 7.5% and 10.0%. The proposed approach provides a good estimate of the sought material properties. It is envisaged that this approach can become of assistance in the evaluation of the material properties for multilayer coatings and small devices.