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Topographic and phase imaging in tapping mode atomic force microscopy (TMAFM) has been performed to investigate the effect of unmodified and modified dual phase fillers on the morphology of and the microdispersion of the filler particles in the rubber matrix. The above fillers were modified using acrylate monomer (trimethylol propane triacrylate, TMPTA) or a silane coupling agent (triethoxysilylpropyltetrasulphide, Si-69) followed by electron beam modification at room temperature. Both unmodified and surface treated fillers were incorporated in a styrene-butadiene rubber. The phase images of the above composites show three levels of contrasts that correspond to matrix, filler aggregates, and bound rubber around the filler aggregates. Also, the images further elucidate the aggregated nature of the filler due to modification, which is more pronounced in the case of electron beam modified acrylated filler loaded rubber. The corresponding topographic images have been characterized by various statistical quantities like roughness parameters and one- and two-dimensional power spectral densities (1D-PSD and 2D-PSD). As compared to the control, significant increase in surface roughness is observed in the case of the modified dual phase filler loaded composites. The higher fractal value of these vulcanizates confirms the above fact. AFM study also suggests that the electron beam modification of the above fillers significantly increases the filler-filler and filler-polymer interactions.