This paper focuses on the spectral analysis of fiber Bragg gratings written in nanostructured large mode area and few-mode fibers when fundamental and higher mode(s) are simultaneously excited. For this purpose, an advanced numerical tool was developed and validated. A method for modal decomposition and superposition was proposed, which overcomes the limitations of commercial software. In the presented approach, the intermodal coupling as a consequence of non-ideal fringe pattern spatial distribution in fiber Bragg gratins is also considered. The numerical tool increases the versatility of fiber Bragg grating spectral analysis, especially taking into account the unconventional optical fibers having independent photosensitivity and refractive index profiles and few-mode operation.