A method of preparing a self-aligned via on a semiconductor workpiece includes using an integrated sequence of processing steps executed on a common manufacturing platform hosting a plurality of processing modules including one or more film-forming modules, one or more etching modules, and one or more transfer modules. The integrated sequence of processing steps include receiving the workpiece into the common manufacturing platform, the workpiece having a pattern of metal features in a dielectric layer wherein exposed surfaces of the metal features and exposed surfaces of the dielectric layer together define an upper planar surface; selectively etching the metal features to form a recess pattern by recessing the exposed surfaces of the metal features beneath the exposed surfaces of the dielectric layer using one of the one or more etching modules; and depositing an etch stop layer over the recess pattern using one of the one or more film-forming modules.