Transition metal dichalcogenide monolayers have demonstrated a number of exquisite optical and electrical properties. Here, the authors report the optical modification of topographical and optical properties of monolayer MoS2 with femtosecond pulses under an inert atmosphere. A formation of three-dimensional structures on monolayer MoS2 with tunable height up to ≈20 nm is demonstrated. In contrast to unmodified monolayer MoS2, these optically modified structures show significantly different optical properties, such as lower photoluminescence intensity and longer fluorescence lifetime. The results suggest a novel way to modify transition metal dichalcogenide materials for mechanic, electronic and photonic applications.