The structural changes in the surface layer of p-type Cz-Si(001) samples after high-dose low-energy (2 keV) He+plasma-immersion ion implantation and subsequent thermal annealing were studied using a set of complementary methods: high-resolution X-ray reflectometry, high-resolution X-ray diffraction, transmission electron microscopy and atomic force microscopy. The formation of a three-layer structure was observed (an amorphous a-SiOxlayer at the surface, an amorphous a-Si layer and a heavily damaged tensile-strained crystalline c-Si layer), which remained after annealing. Helium-filled bubbles were observed in the as-implanted sample. The influence of annealing on the evolution of the three-layer structure and the bubbles is considered. The bubbles are shown to grow after annealing. Their characteristic size is determined to be in the range of 5–20 nm. Large helium-filled bubbles are located in the amorphous a-Si layer. Small bubbles form inside the damaged crystalline Si layer. These bubbles are a major source of tensile strain in the c-Si layer.