Amorphous Si/SiOx multi-layered films and nanostructures were deposited on Si substrates by the glancing angle deposition technique using Ar ion beam sputtering of a Si sputter target in an intermittent oxygen atmosphere at room temperature. The chemical composition of the samples was characterized by time-of-flight secondary ion mass spectrometry, as well as - for quantifying these first results - by elastic recoil detection analysis using a 200 MeV Au ion beam. The latter method was found to lead to a significant alteration of the sample morphology, resulting in the formation of complex nanometric structures within the layer stacks. In order to investigate these swift heavy ion irradiation induced effects in more detail, a series of experiments was conducted to determine the dominating influences. For this purpose, specific glancing angle deposited multilayered films and nanostructures were irradiated to constant ion fluence with the same 200 MeV Au ion beam at different incidence angles. Scanning electron microscopy of the stacks before and after swift Au ion irradiation revealed considerable changes in film morphology and density as a function of the ion incidence angle, such as an increased porosity of the silicon layers, accompanied by a layer swelling. In contrast, the SiOx layers did not show such effects, but exhibited clearly visible swift heavy ion tracks. The observed effects became stronger with decreasing ion incidence angle.