Thed effects of sputter gas pressure and substrate surface micro-roughness on the microstructure and surface topography have been investigated in the Cu thin films sputter deposited onto polyimide substrates. The surface roughness of polyimide was controlled by oxygen rf plasma treatment. In the Cu film deposited at the pressure of 5 mtorr, the surface is smooth and the columnar structure is not visible regardless of polyimide surface more open boundaries. The polyimide surface roughness enhances these effects, These phenomena can be explained in therm of atomic shadowing effect.