Disclosed methods reduce the discontinuities that between individual layers of a structure that is formed at least in part using electrochemical fabrication techniques. Discontinuities may exist between layers of a structure as a result of up-facing or down-facing regions defined in data descriptive of the structure or they may exist as a result of building limitations, e.g., those that result in non-parallel orientation between a building axis and sidewall surfaces of layers. Methods for reducing discontinuities may be applied to all regions or only to selected regions of the structure. Methods may be tailored to improve the accuracy between an original design of the structure and the structure as fabricated or they may simply be used to smooth the discontinuities between layers. Methods may include deposition operations that selectively favor filling of the discontinuities and/or etching operations that selectively favor removal of material from protrusions that define discontinuities.