Thin films of cobalt (10, 40, and 100 nm) are deposited on Si substrate by electron beam physical vapor deposition technique. After deposition, 4 pieces from each of the wafers of silicon substrate were cut and annealed at a temperature of 200°C, 300°C, and 400°C for 2 hours each, separately. X‐ray diffraction, atomic force microscopy, and transmission electron microscopy (TEM) are used to study the structural and morphological characteristics of the deposited films. To obtain TEM images, Co films are deposited on Cu grids; so far, no such types of TEM images of Co films are reported. Structural studies confirm nanocrystalline nature with hexagonal close packed structure of the deposited Co film at lower thickness, while at higher thickness, film structure transforms to amorphous with lower surface roughness value. The particle sizes in all the cases are in the range of 3 to 5 nm. Micro‐Raman spectroscopy is also used to study the phase formation and chemical composition as a function of thickness and temperature. The results confirm that the grown films are of good quality and free from any impurity. Studies show the silicide formation at the interface during deposition. The appearance of new band at 1550 cm−1 as a result of annealing indicates the structural transformation from CoSi to CoSi2, which further enhances at higher annealing temperatures.