Diploma thesis deals with ageing process of thin films of Co and Cu on Si substrate, prepared by the IBAD method. The process of film ageing, which depends on time of exposition to the atmosphere at room conditions, was investigated with spectroscopic ellipsometry (VIS+UV) and atomic force microscopy. In case of thin Co films, approximately four days long incubation period was observed. During this time period, a change in the optical parameters of the film occurs without a measurable change of the film topography. Using non-contact atomic force microscopy, a growth of the transitional film in the island growth regime was observed. During the ageing of thin Cu films, two stages of growth of the transitional layer were observed - nucleation stage and growth stage. Both of these time periods of the transitional layer growth show direct logarithmic dependence. Using non-contact atomic force microscopy, the growth of the transitional film was observed. Using atomic force microscopy in non-contact regime, time dependent measurement was done and the process of forming of one monolayer of the transitional layer was documented. Within the diploma thesis, a series of experiments on ultra high vacuum system were performed in order to investigate phase transformation of thin Fe films (22 monolayers) on Cu(100) stabilized by CO absorption. The transformation from fcc phase to bcc phase was induced by Ar+ ion beam bombardment with the ion energy in the range (0.5-4) keV. The process of phase transformation was observed by surface magneto-optic Kerr effect, Auger electron spectroscopy and low energy electron diffraction.