A method of filling a trench includes: providing a substrate having an upper surface, and a trench extending therein from the upper surface; forming a deposition layer on the substrate in a manner in which the layer partially fills the trench and has a portion which overhangs the trench at the upper surface of the substrate; etching, in a processing chamber, the portion of the deposition layer which overhangs the trench, including by inducing a reaction in the processing chamber using plasma; and subsequently depositing material on the substrate within the partially filled trench, including by inducing a reaction in the processing chamber using plasma.