Strictly-speaking, the band structure is uniquely defined for a perfectly-periodic crystal structure only; this is why there is no band structure analyzer for device configuration.
I guess the band diagram you are referring to is that given by the Hartree Difference Potential (HDP) as discussed in the following tutorial
http://docs.quantumwise.com/casestudies/ag_si_interface/ag_si_interface.html. So, you will need to compute the HDP for your device structure, and the HDP curve can then be considered as a visualization for how the conduction (valence) band minimum (maximum) changes across the device.
In the vacuum, the HDP goes to a constant that defines the vacuum level, and you can calculate the Fermi energy with respect to this level.