The cobalt thin films are grown by D.C. magnetron sputtering as a function of the target-to-substrate distance, bias and power on both Si (100) and (111) substrates. The crystal structure and morphology of the thin films are characterized by 4-point probe, x-ray diffraction, scanning electron microscopy, transmission electron microscopy and atomic force microscopy. It is found that the cobalt crystal structure can be varied from HCP to FCC by varying the target to-substrate distance from 6 to 10 cm. The resistivity, roughness and the preferred orientation of the thin films are greatly affected by the substrate bias and power. The lowest resistivity of Co films is 9.8 -cm when deposited at the target to-substrate distance of 6cm, the applied power of 50W and the substrate bias of -75 volts. In addition, pyramid-like nanostructures with sharp tips are formed on the surface of the thin films when negative bias is applied. The faceted planes on the nanostructures depend on the resulting Co crystal structure while the size and density are determined by the growth parameters. The evolution of the surface nanostructures are systematically examined as a function of substrate bias and thin film thickness. The formation mechanism of the surface nanostructures is discussed in the paper.