The main goal of the present study was to produce insights from the atomistic modeling into the structural changes in elastomer-based polymer nanocomposites caused by the surface modifications of the filler particles, and by the crosslinking of the participating polymer matrix. The fully atomistic molecular-dynamics computer simulations of crosslinked (1,4) cis-polyisoprene (PI) films capped by amorphous silica substrates was set-up, in the presence of realistic coupling and covering agents. The PI film stratified structure has been studied in the proximity of the corresponding glass transition, by varying the degree of crosslinking and the PI film thickness. Some monomer ordering induced by the pristine (bare) silica disappeared almost completely in films with modified surfaces. The average monomer density increased with degree of crosslinking. As compared with PI bulk, the glass-transition temperature was slightly larger for highly crosslinked PI films with bare silica and surfaces with coupling agents, and increased with increasing confinement. (c) 2015 Wiley Periodicals, Inc.