Fiber Bragg grating (FBG) inscription methods based on femtosecond laser sources are becoming increasingly popular owing to the (usually) non-linear nature of the index modification mechanism and to the resulting advantages. They allow, for example, fabricating fiber gratings that can survive temperatures exceeding 700°C, which can be an asset in the domain of fiber sensing. However applying femtosecond laser based grating fabrication to microstructured optical fibers (MOFs) can be challenging due to the presence of the air holes in the fiber cladding. The microstructured cladding not only impedes light delivery to the core in most cases, but also causes a non-uniform intensity distribution in the MOF core. To deal with these challenges we present a modeling approach that allows simulating how the reflectivity of the grating and the nature of the index modulation are affected by the inscription conditions. We rely on transverse coupling simulations, empirical data and coupled mode analysis to model the induced index change and the resulting grating reflectivity. For IR femtosecond grating inscription we show that due to the intensity redistribution in the core region, irreversible Type II index changes can be induced in a MOF at laser peak intensities below the Type II threshold for step-index fibers. The resulting non-uniform induced index change has repercussions on the reflection spectrum of the grating as well. Our coupled mode analysis reveals, for example, that although the average index change in the core region can be high, the partial overlap of the core mode with the index change region limits the reflectivity of the grating.