A method and system for drilling holes in a repaired composite structure. Four corner holes are selected from holes outside of a repaired area in the repaired composite structure. The four corner holes define a rectangle encompassing the repaired area with sides that each include a pair of corner holes with intermediate holes in between. A surface representation is generated based on a scan of the repaired composite structure that includes the rectangle. Side hole locations between a corresponding pair of corner holes are generated for each side of the rectangle. Grid vector lines are generated between corresponding pairs of side hole locations on opposite sides of the rectangle. The grid vector lines intersect each other at intersection points on the surface representation. Point coordinates are determined for intersection points that lie within the repaired area. A path is created for drilling holes at point coordinates for the intersection points.