The concept of the Fermi level is applicable on every solid material. It is the consequence of the statistics of the electron distribution on the available energy levels in the material. The Fermi function defines the probability of occupation of an energy level in a material with electrons. Ma be it is difficult to determine the position not the Femilevel in a material. Organic semiconductors have valence band and also they have a conduction band resulting from overlap of the homo and lumo energy levels of the material molecules. The narrow nature of these bands specially the lumo band does not mean the nonexistence of the fermilevels.
On the other side for such materials, there distinguished energy levels are referenced to vacuum level Ev. Therefore, it is more interesting to define the electron affinity rather than the workfunction. he electron affinity is the difference between the the vacuum level and the lumo level while the workfunction is energy difference between the the vacuum level and the fermilevel.
I am trying to make a schottky junction between metal and organic semiconductor so I have to choose work function of metal according to work function of organic semiconductor. Is it permissible to assume Ef in middle?
As long as the material is not either p type or n type, so it is intrinsic and consequently its fermilevel can be assumed to be in the middle of the energy gap. Concerning the MS contacts, the position of the fermilevel at the surface of the material can be pinned at specific level because of the presence of high density of allowed surface states in the energy gap.
For more very useful information about the MS contacts with organic semiconductors please follow the Link: