Dear Vipul,

This is an old problem in semiconductor physics. In summary you need 2 set of 
calculations. One for a surface (interface) and another one for bulk.

Key papers to review are:

http://journals.aps.org/prb/abstract/10.1103/PhysRevB.35.8154

http://journals.aps.org/prl/abstract/10.1103/PhysRevLett.61.734


There are many modern examples as well. In my opinion absolute alignment to 
vacuum is more difficult than aliment of material 1 to material 2.


Best Regards,
Mostafa
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