Holes through a PCB are typically drilled with small-diameter drill bits made of solid coated tungsten carbide. Coated tungsten carbide is recommended since many board materials are very abrasive and drilling must be high RPM and high feed to be cost effective. Drill bits must also remain sharp to not mar or tear the traces. Drilling with high-speed-steel is simply not feasible since the drill bits will dull quickly and thus tear the copper and ruin the boards. The drilling is performed by automated drilling machines with placement controlled by a drill tape or drill file. These computer-generated files are also called numerically controlled drill (NCD) files or "Excellon files". The drill file describes the location and size of each drilled hole. These holes are often filled with annular rings (hollow rivets) to create vias. Vias allow the electrical and thermal connection of conductors on opposite sides of the PCB.

When very small vias are required, drilling with mechanical bits is costly because of high rates of wear and breakage. In this case, the vias may be evaporated by lasers. Laser-drilled vias typically have an inferior surface finish inside the hole. These holes are called micro vias.

It is also possible with controlled-depth drilling, laser drilling, or by pre-drilling the individual sheets of the PCB before lamination, to produce holes that connect only some of the copper layers, rather than passing through the entire board. These holes are called blind vias when they connect an internal copper layer to an outer layer, or buried vias when they connect two or more internal copper layers and no outer layers.

The walls of the holes, for boards with 2 or more layers, are made conductive then plated with copper to form plated-through holes that electrically connect the conducting layers of the PCB. For multilayer boards, those with 4 layers or more, drilling typically produces a smear of the high temperature decomposition products of bonding agent in the laminate system. Before the holes can be plated through, this smear must be removed by a chemical de-smear process, or by plasma-etch. Removing (etching back) the smear also reveals the interior conductors as well.