A semiconductor device has a semiconductor wafer and a conductive via formed through the semiconductor wafer. A portion of the semiconductor wafer is removed such that a portion of the conductive via extends above the semiconductor wafer. A first insulating layer is formed over the conductive via and semiconductor wafer. A second insulating layer is formed over the first insulating layer. The first insulating layer includes an inorganic material and the second insulating layer includes an organic material. A portion of the first and second insulating layers is removed simultaneously from over the conductive via by chemical mechanical polishing (CMP). Alternatively, a first insulating layer including an organic material is formed over the conductive via and semiconductor wafer. A portion of the first insulating layer is removed by CMP. A conductive layer is formed over the conductive via and first insulating layer. The conductive layer is substantially planar.