The focused ion beam (FIB) is a powerful tool for rapid prototyping and machining of functional nanodevices. It is employed regularly to fabricate test metamaterial structures but, to date, has been unsuccessful in fabricating metamaterial structures with features at the nanoscale that rely on surface phonons as opposed to surface plasmons because of the crystalline damage that occurs with the collision cascade associated with ion sputtering. In this study, we employ a simple technique of protecting the crystalline substrate in single-crystal 4H-SiC to design surface phonon polariton-based optical resonance structures. By coating the material surface with a thin film of chromium, we have placed a material of high sputter resistance on the surface, which essentially absorbs the energy in the beam tails. When the beam ultimately punches through the Cr film, the hard walls in the film have the effect of channeling the beam to create smooth sidewalls. This demonstration opens the possibility of further rapid-prototyping of metamaterials using FIB.