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Multilayer thin films consisting of alternating pure molybdenum and silicon layers with layer thicknesses of a few nanometers are of increasing interest for soft X-ray optical applications in the wavelength region above the Si-L edge [Lambda] = 12.4 nm. In order to enhance the thermal and long term stability, which is of great importance for applications with high power soft X-ray sources, interdiffusion of molybdenum and silicon as a mechanism of thermal destruction of the multilayer system has to be reduced. For this purpose multilayers with absorber layers of two different MoxSi1-x mixtures, Mo0.5Si0.5/Si and Mo0.33Si0.67/Si, and a double-layer thickness of about 7 nm are prepared by electron beam evaporation in a UHV system. The thermal stability for both systems is studied by post deposition annealing at different temperatures. For each temperature interdiffusion and interfacial roughness of the multilayers are examined by small angle X-ray diffraction [SAXD] at [Lambda] = 0.154 nm, while the formation of nanocrystallites with lattice plane orientation parallel to the layer system is investigated by large angle X-ray diffraction [LAXD]. In the case of the Mo0.5Si0.5/Si multilayer system these studies are completed by high resolution transmission electron microscopy [HRTEM] at multilayer cross sections and optical diffraction measurements [ODM].