A self-aligned via process to prevent the via poisoning includes forming a hydrogen silsesquioxane layer on the substrate and over a pre-formed metal layer, forming an etching stop layer on the hydrogen silsesquioxane layer, forming an oxide layer on the etching stop layer, and then proceeding with a two-step etching process to form a via. The two-step etching process first patterns the oxide layer using a patterned photoresist layer as a mask, and then patterns the etching stop layer together with the hydrogen silsesquioxane layer using the patterned oxide layer as a mask. Because the etching stop layer prevents the hydrogen silsesquioxane layer from reacting with the oxygen plasma during the photoresist layer removal process, via poisoning is eliminated.