A very stable approach for finding optical resonances is to solve an eigenvalue equation that evolves from the linearization of the inverse scattering matrix. In this paper, we show how to use this approach in the Fourier modal method so that advanced coordinate transformation methods such as adaptive spatial resolution and matched coordinates can be included. Furthermore, we present a way that accelerates the computation of the inverse scattering matrix tremendously and allows the derivation of the resonant field distribution inside the structure efficiently.