Methods for forming three-dimensional transistor devices. In one embodiment a method of forming a three-dimensional transistor device may include providing a substrate comprising a semiconductor device structure, the semiconductor device structure comprising a nanowire stack, a gate stack disposed above the nanowire stack, and an inner spacer layer, disposed over the gate stack and the nanowire stack. The method may further include directing ions at the semiconductor device structure, wherein an altered layer is formed in a first part of the inner spacer layer, and an unaltered portion of the inner spacer layer remains, subjacent to the altered layer.