A method and apparatus for installing alignment of fastener assemblies. The method comprises placing an alignment tool on a reference datum. The method also takes pitch, roll, and yaw readings from an instrument associated with the alignment tool. Further, the method positions the alignment tool relative to a number of holes. Still further, the method adjusts the alignment tool based on pitch, roll, and yaw readings. The method also installs a first fastener assembly relative to a first hole of the number of holes.