A method of forming an etch stop layer 40 above a fuse 16 in a fuse opening (or window) 92 using a specialized 2 stage etch process. The invention has two important features: First, the etch stop layer 40 is formed from a polysilicon layer (P2 or P4) that is used to fabricate semiconductor devices on a substrate. The etch stop layer 40 is preferably formed of polysilicon layer to is used to from a contact to the substrate 10 (P2) or to form part of a capacitor (P4). Second, a specialized two stage etch process is used where the second stage etches the etch stop layer 40 while simultaneously forming a passivation layer 114 over a metal pad 85. The method comprises: forming fuses 16 over said isolation regions 10 over the fuse area 15; forming a first dielectric layer 30 overlying the fuses 16; forming an etch stop layer 40 over the first dielectric layer 30; forming an insulating layer 43 over the etch stop layer; forming a fuse opening 92 in the insulating layer 43 by etching, in a first etch stage, thorough fuse photoresist openings 90A and stopping the first etch stage on the etch stop layer 40; and etching though the etch stop layer 40 in the fuse opening 92 in a second etch stage.