The focused helium ion beam microscope is a versatile imaging and nanofabrication instrument enabling direct-write lithography with sub-10 nm resolution. Subsurface damage and swelling of substrates due to helium ion implantation is generally unwanted. However, these effects can also be leveraged for specific nanofabrication tasks. To explore this, we investigate focused helium ion beam induced swelling of bulk crystalline silicon and free-standing amorphous silicon nitride membranes using various irradiation strategies. We show that the creation of near-surface voids due to helium ion implantation can be used to induce surface nanostructure and create subsurface nanochannels. By tailoring the ion dose and beam energy, the size and depth of the swollen features can be controlled. Swelling heights of several hundred nanometers are demonstrated, and for the embedded nanochannels, void internal diameters down to 30 nm are shown. Potential applications include the engineering of texturized substrates and the prototyping of on-chip nanofluidic transport devices.