Transmission electron microscopy (TEM) has been used to investigate the effects of room temperature 6 keV helium ion irradiation of a thin (≈55 nm thick) tri-layer consisting of polycrystalline Si, silica, and single-crystal Si. The ion irradiation was carried out in situ within the TEM under conditions where approximately 24 of the incident ions came to rest in the specimen. This paper reports on the comparative development of irradiation-induced defects (primarily helium bubbles) in the polycrystalline Si and single-crystal Si under ion irradiation and provides direct measurement of a radiation-induced increase in the width of the polycrystalline layer and shrinkage of the silica layer. Analysis using TEM and electron energy-loss spectroscopy has led to the hypothesis that these result from helium-bubble-induced swelling of the silicon and radiation-induced viscoelastic flow processes in the silica under the influence of stresses applied by the swollen Si layers. The silicon and silica layers are sputtered as a result of the helium ion irradiation; however, this is estimated to be a relatively minor effect with swelling and stress-related viscoelastic flow being the dominant mechanisms of dimensional change.