A method and apparatus for optimizing the drilling position of a multi-layer printed circuit board prior to drilling. A template having precisely located target holes and fixture reference marks provides initial coordinate reference information for multi-layer printed circuit boards to be inspected by x radiation. Each board is processed by insertion into a holding fixture, examination of four quadrant target areas using x-ray sources and detectors, digitization of the target area images in each quadrant, and computaton of the optimum board position in a follow-on drilling apparatus. After optimization, three reference holes are punched along one edge of the board to provide accurate fiducial positioning marks when the board is placed in the drilling apparatus.