A photo resist layer is used to protect a dielectric layer and conductive elements embedded in the dielectric layer when patterning an etch stop layer underlying the dielectric layer. The photo resist layer may further be used to etch another dielectric layer underlying the etch stop layer, where etching the next dielectric layer exposes a contact, such as a gate contact. The bottom layer can be used to protect the conductive elements embedded in the dielectric layer from a wet etchant used to etch the etch stop layer.