In this article, we present novel sample preparation methods using a helium ion microscope (HIM). We report the possibility of reshaping, at room temperature, thin metal lines on an electron-transparent membrane: A set of platinum bridges with standard geometry (300 × 200 × 15 nm) was modified at room temperature into different shapes using focused helium (He)-ion beam. Also the applicability of the HIM as a tool for precise modification of silicon (Si) and strontium titanate (SrTiO3) lamellae is shown and discussed. We demonstrated that in situ heating (e.g., at 600 °C) of the samples during He-beam illumination by use of a specially developed heating stage enables production of thin Si and SrTiO3 samples without significant artifacts. The quality of such cuts was inspected by transmission electron microscopy with high-resolution imaging, and the diffraction patterns were analyzed. Copyright © Materials Research Society 2013.