In a structure that guides elastic waves, a discontinuity (defect, shape variation) causes scattering (reflection, partial extinction or mode conversion). Two modal formulations have been developed to link separate models dealing with the calculation of the modal decomposition, with the generation and reception of guided waves (GW), with their scattering. The first concerns pulse-echo configurations (involving a single transducer), the other concerns pitch-catch configurations (two transducers involved). A new finite element (FE) method has been developed to compute the scattering by an arbitrary discontinuity, based on the modal decomposition of the field. Perfectly transparent boundary conditions (Dirichlet-to-Neuman boundaries) are developed, allowing the FE computation zone to be reduced to a minimum. A specific variational problem including these boundary conditions was obtained and solved using FE tools. By combining the modal formulations, the new FE scheme and tools for GW radiation, propagation and reception based on the Semi-Analytical Finite Element (SAFE) method, a new simulation tool has been developed. It can address almost arbitrary configurations of GW nondestructive testing. Moreover, a source inside the FE computation zone can be defined so that configurations of testing by acoustic emission can also be simulated. Examples of use of this tool are shown, some dealing with junctions of complex geometry between two guides, other with surface or bulk sources of acoustic emission.