I want to calculate the heat transfer in a solid material, a 3D-model that has the shape of a thick bowl. I know the temperature on the outer surface and want to calculate the temperature on the inner surface, from measurements I also know the temperature at a number of points inside the material and the heat flow from the outer wall (this could be considered as an inverse heat transfer problem). I want to use these measured values as boundary conditions, can I apply boundary conditions to certain points?

It is possible to use these points to calculate isotherms, then maybe I could use the isotherms as walls with constant temperature, if that makes the problem easier?

If you set the (known) temperature on the outer wall and set a reasonable estimate for the heat transfer coefficient for the internal surface you should get reasonable results.

You can then use your internal temperature measurements and outer wall flux for validation purposes.