Disclosed in a method of planarizing a silicon on insulator (SOI) structure. The invention performs a first chemical mechanical planarization (CMP) process on an insulator (e.g., oxide) layer. However, this first CMP process creates scratches on the insulator layer. The invention forms a polish stop insulator (e.g., nitride) over the insulator layer in, for example, a liquid phase chemical vapor deposition (LPCVD) process. The polish stop insulator fills in the scratches. The invention then forms an opening through the insulator layer and through the polish stop insulator (e.g., in a reactive ion etching (RIE) process) and deposits a conductor within the opening. The invention performs a second CMP process on the conductor. The polish stop insulator is harder than the insulating layer and prevents the second CMP process from scratching the insulator layer. The invention removes portions of the polish stop insulator to leave the polish stop insulator only within the scratches. The polish stop insulator within the scratches prevents short circuits across said insulator layer.