The method and apparatus for drilling holes and optionally inserting fasteners of the present invention provide for efficiently drilling holes through a multiple-layer structure because the layers are securely held together during the drilling by an electromagnet and a clamp, each on opposite sides of the structure. The electromagnet and clamp hold the layers together so tightly that burrs do not form within the holes and debris does not accumulate between the layers and, therefore the layers do not have to be disassembled after drilling. In addition, the apparatus and method of the present invention provide for initially drilling the hole with a countersink and for inserting a fastener into the hole, through the electromagnet, immediately after drilling the hole, such that the hole does not have to be revisited after reassembly and drying of the sealant in order to drill a countersink and/or insert a fastener.