It is likely that MW irradiation will simply heat biofuel. I don't see another possible non-thermal effect that could change the properties of biofuel.
If you know the specific absorption rate (SAR) of the biofuel and the MW irradiance level, you can certainly have an idea of the temperature change.
You can compare a sample of biofuel heated by MW irradiation and a similar sample heated in a conventional climatic chamber. They should behave identically ! If not, there is something to investigate...
Electromagnetic Biostimulation of Living Cultures for Biotechnology, Biofuel and Bioenergy Applications Ryan W. Hunt 1,*, Andrey Zavalin 2, Ashish Bhatnagar 1, Senthil Chinnasamy 1 and