Effect of the kind of nano-fillers on dynamic mechanical properties and morphology of the filler loaded crosslinked natural rubber (NR) is reviewed, where carbon black (CB), hydrophobic silica and hydrophilic silica are compared. 3D-TEM/electron tomography is utilized to measure a closest distance (d_p) between centers of two neighboring nano-filler aggregates. Activation energies (ΔE_J' and ΔE_J") are calculated from temperature dependences of storage compliance (J') and loss compliance (J") of the filler loaded cross-linked NRs and are discussed with the d_p values. An interaction layer between the nano-fillers and NR is suggested to be additionally composed of at least two layers with different viscoelastic energy levels. For the samples with CB loadings of 30 parts per one hundred rubber by weight or more, the CB/NR interaction layer (CNIL) is visualized by 3D-TEM, and the CNIL is proposed to be an origin of reinforcement effect using the parallel mechanical model.