Nonlinear ultrasonic guided waves are among the most promising new tools for early stage damage detection owing to their high sensitivity and long-range propagation features. However, signatures from instrumentation, transducers, and couplant effects create false positives mixing with the material- or defect-induced nonlinearities, leading to inaccurate measurements. Here, we propose a novel technique using a waveguide metamaterial rod, which acts as a mechanical acoustic filter for suppression of higher harmonic components in the measured signal. The proposed waveguide metamaterial consists of an array of flat axisymmetric ridges arranged periodically on the surface of the rod. It is experimentally demonstrated that the higher harmonic components are filtered when the proposed metamaterial rod is placed at the transmission side, thus removing unwanted nonlinearities from the received signal in a pitch-catch configuration. Furthermore, the application of this method is demonstrated by detecting a discontinuity in the workpiece through its nonlinear response enhanced using the metamaterial. This technique is attractive for early stage material diagnosis in engineering, biomedicine, and health monitoring of critical engineering assets. © 2021 Author(s).