The question you may also ask, related to this, is, how would we absorb this cosmic waves to put it into the food. In general, high energy cosmic waves, have two undesirable properties, first they are so ultra-energetic that every normal protein chains or related organic material to life exposed to it is denatured. Secondly, they are very rare and have very small energy density in the low atmosphere.
As about the microwave oven itself, the process of heating food, as long as (normally) most of the food constituent is water, has to do with vibrate the waters molecules by resonance with their "normal" vibration frequency... This water molecules vibrations, heats the food through loosing this energy via friction with other food molecules. (But Im sure you can find more complete answers along this forum, in related topics, as suggested).