Ostensibly, it is the area of a fiber bundle through which the light is actually transmitted as opposed to the structure and gaps between individual fibers in which light is not transmitted.
You mean cross-sectional area?
If so, to find this quantity it would be governed by your input beam width I assume, since the physical core area will be larger than the effective core area?
If my above comments are right, then do I need to find the FWHM of my beam and use that to calculate the cross sectional area?
My initial thought on "effective core area" seems incorrect. The following talk about "effective core area of one fiber", but I believe my thought on the cross-sectional area that transmits light as opposed to the structural or physical fiber cross-sectional area as being the "effective core area" seems correct.
Relationship between nonlinear effective core area and backscattering capture fraction for single mode optical fibres
http://ieeexplore.ieee.org/Xplore/login.jsp?url=/iel1/2220/10465/00491076.pdf?arnumber=491076