Some embodiments of the present invention provide processes and apparatus for electrochemically fabricating multilayer structures (e.g. mesoscale or microscale structures) with improved endpoint detection and parallelism maintenance for materials (e.g. layers) that are planarized during the electrochemical fabrication process. Some methods involve the use of a fixture during planarization that ensures that planarized planes of material are parallel to other deposited planes within a given tolerance. Some methods involve the use of an endpoint detection fixture that ensures precise heights of deposited materials relative to an initial surface of a substrate, relative to a first deposited layer, or relative to some other layer formed during the fabrication process. In some embodiments planarization may occur via lapping while other embodiments may use a diamond fly cutting machine.