An x-ray confocal defect detection system comprises an x-ray source, a confocal component, and defect detectors and operates on a target portion of a semiconductor device. The x-ray source generates x-ray energy. The semiconductor device includes a plurality of formed layers. The target portion is a selected layer or portion of the plurality of formed layers. At least a portion of the x-ray is transmitted through the semiconductor device as transmitted x-ray. The confocal component receives the transmitted x-ray and passes target x-ray intensity from the target portion of the transmitted x-ray energy. Detectors receive the target x-ray from the confocal component from which defect analysis can be performed.