A good dispersion of silica in a rubber vulcanizate is important as it influences the filler-to-rubber interaction and consequently the final properties. This article presents an investigation into the morphology of silica-reinforced natural rubber (NR) in the presence and absence of a silane coupling agent, bis(triethoxysilylpropyl) tetrasulfide (TESPT). Micro- and nano-dispersion morphologies of silica in NR and deproteinized natural rubber (DPNR) are studied by using atomic force microscopy (AFM). Using a special network visualization technique based on transmission electron microscopy (TEM), insight into the silica and rubber interaction in the NR and DPNR is gained. In the absence of silane, vacuoles around the silica particles are formed as a result of a weak filler–polymer interaction, whereas the presence of silane leads to strong filler-to-rubber bonding, which prevents formation of vacuoles. Improvement of the micro-dispersion of silica in the NR and DPNR vulcanizates with the use of TESPT is observed from AFM phase imaging. The correlation between the filler-to-rubber interaction as analyzed by TEM and AFM and bound rubber contents as well as the Payne effect is discussed.