I do not know of any software, free or otherwise, but you can figure out the heating profile yourself:
Basically microwave is electromagnetic radiation and the absorption will be like a simple exponential profile from the surface. The heat produced will be proportional to the microwave radiation absorbed and this will be reflected in the temperature profile. However, with time the heat will start to diffuse and will follow the same diffusion law (well, heat propagation follows the same diffusion equations). In one dimension, this is rather simple but can be complicated in three dimension.