A method of etching a trench in a substrate is provided. The method repeatedly alternates between using a fluorine-based plasma to etch a trench, which has trench sidewalls, into a selected region of the substrate; and using a fluorocarbon plasma to deposit a liner on the trench sidewalls. The liner, when formed and subsequently etched, has an exposed sidewall surface that includes scalloped recesses. The trench, which includes the scalloped recesses, is then bombarded with a molecular beam where the molecules are directed on an axis parallel to the trench sidewalls to reduce the scalloped recesses.