Nanocomposite materials are receiving increased attention for potential applications including magnetic storage media, high-surface-area catalysts, selective membranes, and photonic band gap materials, etc. Their role in more conventional applications is still relevant in many different fields. In fact, this combination of classical organic polymers or hybrid organic/inorganic matrices and nanoparticles can lead to the enhancement of mechanical, optical, thermal, fire-retardant, and ablative properties, as well as gas-transport properties compared to either of the individual components). In particular, due to the ability to microphase separating into a variety of ordered structures on nanometric length scales, these matrices can be used as ordered template to afford opportunities for controlling the spatial and orientational distribution of nanoparticles to lead to new materials with tailored microstructure-dependent properties. Whatever the matrix, it is of paramount importance to describe the fundamental phenomena that leads to the microstructure at nanoscale level and, for achieving this result, it is necessary to resort to multiscale molecular modeling. The microphase behavior of complex nanoparticle systems may be described by mesoscale simulation methods. Among these, a particle based (DPD) method is chosen here for the description of the system since it considers beads of different types and different dimensions that allow us to simulate both the enthalpic and entropic effect of the nanoparticles embedded in a polymeric matrix. Having obtained a realistic morphology at mesoscale, it is possible to transfer the simulated mesoscopic structure to finite elements modeling tools (FEM) for calculating macroscopic properties for the systems of interest. If all these methods are tightly integrated, a complete, multiscale molecular modeling (M3) recipe for studying and characterizing these materials is obtained. In this paper we apply this procedure to systems made up by different polymeric and hybrid organic/inorganic matrices filled with nanoparticles of different chemical nature, size, and shape, thus accounting for both enthalpic and entropic factors. We will present an integrated multiscale method that starts at atomistic level with the determination of the interactions energies between the components involved, passes this information to the mesoscale level where the morphology is simulated including the embedded particles, and finally the macroscopic properties are calculated with a finite elements method. Simulated data at each single scale will be compared with experimental information to validate the methodology.