There is a significant need to understand solid-liquid interactions at nanoscale to determine the fluid behavior in several revolutionary applications. Specifically, nanoscale surface wetting, nanoscale liquid transport, and nanoscale heat transfer are the most sought-after subjects in recent scientific and industrial applications. This thesis focuses on characterization and possible control of wetting, fluid flow, and heat transfer using nanoscale surface structures. First, wetting behavior on a nanostructured surface was studied to resolve contact angle hysteresis. The droplet was found stabilized at a metastable state with a contact angle significantly different from its equilibrium value due to contact line pinning from the surface asperities. The contact angle was found to increase linearly by increasing droplet size when the droplet is pinned. However, these pinning effects become negligible, and the contact angle reaches the equilibrium value of the corresponding surface when the surface structure size becomes negligible compared to droplet size. Second, fluid flow in nanostructured nanochannels was studied to determine the transport behavior. While the slip boundary condition on a smooth surface correlated with the wetting angle, transport in a nanostructured channel remained mostly independent from wetting condition of the corresponding surface structure. Lastly, droplet evaporation over nanopatterned surfaces was investigated. When the droplet temperature reached the Leidenfrost point, a sudden increase in the interface thermal resistance was observed, which significantly decreased the heat transfer to the droplet. Increasing the size of the surface structure pushed the Leidenfrost point to higher surface temperatures. Current results contribute to various disciplines in engineering and applied sciences. Keywords and Phrases: Surface patterning, Molecular Dynamics, Wetting, Pinning, Slip Length, Interfacial Thermal Resistance, Droplet Evaporation, Leidenfrost Phenomena