For now you can export the individual field component files (f3d files) from OptiFDTD analyzer and then process them in Matlab for example.
So, if you have an observation area recording the Ex, Ey and Ez components, after simulation, go to OptiFDTD analyzer in Tools-> Detector analyzis -> Observation Area. Then click on Export Data and select the Ex, Ey and Ez components.
You will have 3 files corresponding to Ex, Ey and Ez components. You can open these files in Matlab for example and do some calculations on them. For example:
E = sqrt(abs(Ex).^2 + abs(Ey).^2 +abs(Ez).^2)
This will give you the |E| value.
To obtain E0, run another simulation without your structure to make a reference and do the same.
From next release of OptiFDTD (latter this summer), we will provide a script function outputting the |E| value directly to file. You will also be able to perform calculations directly from the script editor in OptiFDTD.