Systems and methods for inertial reference system alignment are provided. In certain embodiments, a system comprises an inertial reference system, the inertial reference system providing motion measurements; and a processing system coupled to receive the motion measurements from the inertial reference system. Further, the processing system is configured to execute instructions that direct the processing system to identify one or more frequencies in the spectrum of the motion measurements that are associated with vibrations; attenuate the motion measurements at the one or more frequencies; and use the attenuated measurements to aid in the production of navigation information.