A method of patterning a substrate includes receiving a substrate having microfabricated structures, including mandrels; executing a deposition process that deposits a first material on the mandrels, the deposition process including cyclically moving the substrate through a set of deposition modules. The substrate is moved through the set of deposition modules so that the first material is deposited at a first thickness at top portions of the mandrels and at a second thickness at bottom portions of mandrels, the first thickness being greater than the second thickness. The method includes executing a spacer deposition process that conformally deposits a second material on the substrate; executing a spacer open etch that removes depositions of the second material from over a top surface of the mandrels; removing the first material and the mandrels from the substrate, leaving sidewall spacers; and transferring a pattern defined by the sidewall spacers into an underlying layer.