The microdispersion of silica in filled elastomer vulcanisates was evaluated by transmission electron microscopy (TEM)—network visualisation analysis. In this study, the silica is modified with a wide range of coupling and non-coupling silanes. The silica-filled elastomer samples were microtomed using a glass knife. The resulting TEM micrographs were interpreted and characterised based on aggregates with a cross-sectional area larger than 100 nm2. The study showed that silica surface modification has reduced the silica aggregate size by approximately 30–40% compared to an untreated silica-filled elastomer vulcanisate. The TEM micrographs showed evidence of coupling between silica and the elastomer phase and demonstrated a good estimation of silica microdispersion in the elastomer phase. This study has shown that the presence of different surface functionalities has an effect on the silica microdispersion.