In this paper, the technique of irradiation of thin films by Ga+ ions inside of scanning electron microscope, by a focused ion beam is developed. The influence of irradiation on magnetic properties of thin epitaxial films of Co, grown by molecular beam epitaxy in ultrahigh vacuum on a silicon surface with a intermediate layer of copper atoms. It has been shown that low radiation doses lead to an increase of magnetic hardness of the samples. At higher doses, there is a decrease of coercive force, which is apparently due to a change of crystalline structure of the material. An interesting fact is that in the dose range of 1012-1015 the relative remanences is practically unchanged and only at higher doses the magnetic properties of the film worsen.