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This paper describes a numerical method to compute van der Waals force between complex and freely oriented objects that have rough surfaces. The force calculation is implemented using the surface formulation of the force. First, the interacting surfaces are approximated with triangular meshes. Then, the surface roughness is taken into consideration by separately adding the asperity heights to each point of the smooth reference surfaces. Three different models are used to describe the rough surfaces: sinusoidal, fractal, and probabilistic. All the three models show considerable reduction in the force values as a function of the roughness peak height or the inclination angle of the surfaces. Despite the reduction of the force values for rough surfaces, van der Waals force is considered to be an essential part when calculating the total interaction force for micromanipulation purposes.