ORIGINAL: Bax

First make sure the airframe is strong enough. Some models just need a thicker firewall that's well-mounted onto the airplane. That's one source of vibration. Single-cylinder engines will never be smooth, but always have some level of vibration. There will also be greater and smaller harmonics, depending upon RPM. That's also a given. If parts of the airframe are breaking due to vibration, not only will they have to be replaced with different materials, but the engine may need work.

It's possible that the engine's prop flange is not quite on center. That would need to be checked. Prop and spinner must be balanced. A vibration-isolating engine mounting system can help. Propping the engine for higher or lower RPM at full throttle can help because it will change the modes of vibration. A heavier or lighter propeller may help. The only way to find out is to try things.