The structural characterization of two-metal phase systems at nanometer scale which present partial or total mixing, is extremely challenging. In the present work, a model to reproduce the x-ray diffraction patterns of multilayers composed by two miscible metals, Mo and W, is presented. Two different deposition conditions were used to obtain different stress states (compressive and tensile). From the proposed model, the contribution of each metal phase was discerned, the intra layer disorder and the level of mixing at the interface were quantified. The comparison between structures deposited sequentially, with others obtained by co-evaporation is also carried out to better understand the details of the interdiffusion and to separate them from the effects of roughness and elastic adaptation stresses. Microstructure characterization by scanning and transmission electron microscopy was compared and discussed with the diffraction analysis.