From my point of view there are two ways you can do that:

1) Calculate a cell of your PCF and by using periodic boundary conditions you will be simulating an infinite crystal without any defect. In that way your fundamental mode will be the cladding effective index.

2) Eliminate the defect in your PCF (for example by putting an air-hole in the core of a conventional PCF). Then calculate the fundamental mode of that structure. I must say this  is a simpler approach, although less accurate. But not much though.

Sorry if I didn't explain myself well enough. I'm not saying you have to model the air-hole structure along with the rest of the cladding. What I mean is to model just the microstructured region as this must give you an approximate result. This approach, as well as yours, is only approximate. The exact solution will be as Birks et al said in their paper,

"The FSM is the fundamental mode of the infinite photonic crystal cladding if the core is absent, so 𝛽FSM is the maximum 𝛽 allowed in the cladding"

that is, to calculate exactly the space-filling mode (FSM) you have to use periodic or infinite conditions.

http://dx.doi.org/10.1364/OL.22.000961