A current challenge of physical, chemical, and engineering sciences is to develop theoretical tools for predicting structure and properties of complex materials from the knowledge of a few input parameters. In this work, we present a general multiscale molecular simulation protocol for predicting morphologies and properties of nanostructured polymer systems and we apply it to three examples of industrial relevance. The first example is of general importance for the polymer industry and is related to the enhancement of mechanical and barrier properties, if a nanofiller is dispersed into a polymer matrix: the role of multiscale modeling for the development of the material in the stage of screening, the best design is evidenced. The second example, important for the optoelectronic industry, is related to the prediction of the dispersion of gold nanoparticles into a diblock copolymer system forming different nanostructures (lamellae, cylinders, ...). In this case, it is relevant to understand how it is possible to influence the self-assembly of the nanoparticles in different regions of the diblock copolymer structure. The third example is of interest to automotive and polymer industries and involves inorganic nanoparticles grafted with organic side chains. The assembly is dispersed in a polymeric matrix and it is interesting to predict the effect of the chain length and grafting density on the nanostructure.