Methods of forming fully aligned vias connecting two metal lines extending in two directions are described. The fully aligned via is aligned with the first metal line and the second metal line along both directions. A third metal layer is patterned on a top of a second metal layer in electrical contact with a first metal layer. The patterned third metal layer is misaligned from the top of the second metal layer. The second metal layer is recessed to expose sides of the second metal layer and remove portions not aligned sides of the third metal layer.