Embodiments include methods and systems of 3D structure fill. In one embodiment, a method of filling a trench in a wafer includes performing directional plasma treatment with an ion beam at an angle with respect to a sidewall of the trench to form a treated portion of the sidewall and an untreated bottom of the trench. A material is deposited in the trench. The deposition rate of the material on the treated portion of the sidewall is different than a second deposition rate on the untreated bottom of the trench. In one embodiment, a method includes depositing a material on the wafer, filling a bottom of the trench and forming a layer on a sidewall of the trench and a top surface adjacent to the trench. The method includes etching the layer with an ion beam at an angle with respect to the sidewall.