Semiconductor device having a through-silicon via and manufacturing method thereof

In a method of manufacturing a semiconductor device, a thermal treatment is performed on a substrate, thereby forming a defect free layer in an upper layer of the substrate, where a remaining layer of the substrate is a bulk layer. A density of defects in the bulk layer is equal to or more than 1×108 cm−3, where the defects are bulk micro defects. An electronic device is formed over the defect free layer. An opening is formed in the defect free layer such that the opening does not reach the bulk layer. The opening is filled with a conductive material, thereby forming a via. The bulk layer is removed so that a bottom part of the via is exposed. A density of defects in the defect free layer is less than 100 cm−3.