Methods and systems for defect repair are disclosed. The methods include: (a) identifying a defect causing an absence of an electrical connection between a first circuit element and a second circuit element, the first and second circuit elements being positioned in or on a substrate and the defect being positioned in the substrate; (b) removing a portion of the substrate to expose the defect, and depositing a conductive material to electrically connect the first and second circuit elements; and (c) verifying that the defect caused the absence of an electrical connection between the first and second circuit elements.