In plasmas in the National Spherical Torus Experiment (NSTX) (Ono et al 2000 Nucl. Fusion40 557) heated with neutral beams, the beam ions typically excite energetic particle modes (or fishbones), and toroidal, global or compressional Alfvén eigenmodes. These modes can redistribute the energetic beam ions, altering the beam driven current profile and the plasma heating profile, or they may affect electron thermal transport or cause losses of the beam ions. In this paper we present experimental results where these instabilities, driven by the super-thermal beam ions, are suppressed with the application of high harmonic fast wave heating.