Evaporation of a nanoscale meniscus on a nano-structured heater surface is simulated using molecular dynamics. The nanostructures are evenly spaced on the surface and rectangular-shaped with a length and height of 0.41 nm and 0.96 nm respectively, and stretching throughout the width of the domain. The simulation results show that the film breaks during the early stages of evaporation due to the presence of nanostructures and no non-evaporating film forms (unlike a previous simulation performed in absence of nanostructures where non-evaporating film forms on the smooth surface). High heat transfer and evaporation rates are obtained. We conclude that heat transfer rates can be significantly increased during bubble nucleation and growth by the presence of nanostructures on the surface as it breaks the formation of non-evaporating film. This will cause additional chaos and allow the surrounding cooler liquid to come in contact with the surface enhancing heat transfer coefficients.