A molecular dynamics simulation of flow over two side-by-side cylinders with atomically rough surfaces is presented. The model is two-dimensional with 3 X 10(5) liquid argon atoms. The surface roughness is constructed by external protrusion of atoms on the surface of the cylinders with specified amplitude and width. Two cylinders, with diameters of d=79.44 (molecular units), are placed at a distance of D in a vertical line. The solids atoms are allowed to vibrate around their equilibrium coordinates to mimic the real solid structure. The influence of various parameters, such as roughness amplitude, topology, periodicity, and the gap between cylinders on the hydrodynamics of flow, especially drag and lift forces, is studied. It was noted that even very little surface roughness, with amplitude on the order of a few nanometers, can influence the drag forces. Both roughness texture and the number of roughening elements affects the drag and lift coefficients. The gap between the cylinders showed to be an effective parameter, especially on the lift force for flow over the nanoscale cylinders.