A silicon-on-insulator (SOI) structure is provided for forming through vias in a silicon wafer carrier structure without backside lithography. The SOI structure includes the silicon wafer carrier structure bonded to a silicon substrate structure with a layer of buried oxide and a layer of nitride separating these silicon structures. Vias are formed in the silicon carrier structure and through the oxide layer to the nitride layer and the walls of the via are passivated. The vias are filled with a filler material of either polysilicon or a conductive material. The substrate structure is then etched back to the nitride layer and the nitride layer is etched back to the filler material. Where the filler material is polysilicon, the polysilicon is etched away forming an open via to the top surface of the carrier wafer structure. The via is then backfilled with conductive material.