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From the books that I read, the discussion and the formulas related to the Fermi Level are always relative to the energy level of Conduction/Valence Band, or Fermi Level in intrinsic semiconductor.

Let's assume that the measurement is done at exact temperature.

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Experimentally, the most straightforward way of measuring this is photoemission spectroscopy. But it is often difficult to measure the position of the Fermi level (chemical potential of the electrons) in an intrinsic semiconductor. The charge carrier distribution is small, and the Fermi level is often pinned by surface states. Also, low conductivity may cause charging.

So most of the comparisons of Fermi levels in doped and intrinsic semiconductors are theoretical.

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