New generation composites using nanoparticle-filled matrices have been significantly broadened to encompass a large variety of one-, two-, and three-dimensional systems made of distinctly dissimilar components mixed at the nanometer scale. Nevertheless, during the fabrication process of these novel composites, many problems potentially could arise. One such problem is the clogging of the channels of the microfiber matrix used due to strong interactions between the nanoparticle additives and the matrix walls. In this paper, a two-dimensional simulation model based on Lagrangian multiphase approach for nanoparticle-filled fluid, which flows around an aligned microfiber matrix, is introduced to investigate and predict the nanoparticles trajectories and their interactions with fluid flow and microfiber walls. An energy “imbalance” technique has been applied between the fluid and the microfiber walls to prevent any potential sticking of the nanoparticle additives on the microfiber walls. The trajectory of the nanoparticle has been predicted by integrating the force balance on it in a Lagrangian reference frame. The governing integral equations for the conservation of mass, momentum and energy have been solved in a segregated numerical fashion by a Control-Volume-Based Finite-Element Method.