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Nanoindentation is one of the most known method for investigating the properties of thin films. The materials can be assessed by means of elastic mechanical properties (hardness and Young's modulus). However, the author's research works show that it is possible to obtain the elastic as well as the plastic material behavior of the investigated thin layer. It can be done by using the nanoindentation experiment and the numerical simulations. This paper focuses then on investigation of thin metal layers by nanoindentation with a support of numerical methods, such as finite element method and numerical optimization processes. Additionally, the 3-level, full factorial design of experiment (DOE) process was applied. In order to carry out such experiment 27 samples were prepared and taken into account: 3 different materials with 3 different thickness's values sputtered on 3 different substrates. The results were then processed by the numerical methods in order to achieve more information about the materials - mainly the plastic behaviour.