To the knowledge of the authors, full-field simulation of filled elastomers accounting for the morphology of their micro-structure has not been carried out. The main goal of the present work is to develop a micro-mechanically motivated finite element model of filler-reinforced elastomers which serves to better understand and quantitatively analyze their complex physical behavior. Deformation-induced changes in the material’s micro-structure like breakage and recovery of bonds (glassy bridges) linking adjacent filler clusters, lead to stress softening in the material. In this work, we demonstrate the effect of various filler concentration and polymer-filler interaction on the morphology of the micro-structure.