We examine the effects of structural changes of solid surfaces on fluid wetting by performing molecular dynamics simulations on a model system. The system consists of a Lennard-Jones fluid confined between two identical solid surfaces under conditions that induce the formation of both a liquid and vapor region. The smooth surface is three layer solid particles arranged in a perfect fee lattice. We represent a molecularly rough surface by adding to the smooth surface a fourth layer consisting of less than a full monolayer of solid particles. This model corresponds to some physical situations where there is surface irregularity, such as surface defects due to vacancies or surface structures caused by adsorption of foreign particles onto a perfect surface. The fluid density profiles near the rough surfaces are different from those near the smooth surface and reflect the detailed molecular structure of the surfaces. More importantly, the changes in surface structure alter significantly the contact angle between the liquid-vapor interface and the solid surface, which is determined by measuring the interfacial tensions between liquid, vapor, and solid phases. The wetting transition on molecularly rough surfaces occurs at a higher value of the liquid-solid interaction strength than that for a smooth surface.