This paper proposes a numerical method to model wave scattering by local inhomogeneities in elastic open waveguides. The damaged zone of the waveguide and its vicinity are described by a finite-element model. This model is coupled on the cross-section boundaries to a modal representation of the field propagating along the waveguide axis in the undamaged parts, yielding transparent boundary conditions. However, open waveguides are unbounded in the transverse direction, which complicates both the numerical resolution and the physical analysis. Theoretically, the wave fields are described by a discrete sum of trapped modes and two continuous sums on radiation modes. The latter is sometimes approximated by a discrete sum of leaky modes, which grow at infinity in the transverse direction. In this paper, a Perfectly Matched Layer (PML) of finite thickness is introduced to absorb outgoing waves in the transverse direction, yielding three types of discrete modes: trapped modes, leaky modes and PML modes (PML modes oscillate mainly inside the layer and are non-intrinsic to the physics). Two numerical test cases are considered: the scattering at the junction between a closed and an open cylindrical waveguides and the scattering by an axisymmetrical notch. Good agreement with literature results is found. In particular, the influence of PML modes on the scattered field is highlighted through numerical tests. Due to the lack of power orthogonality of leaky modes, it is also shown that the modal cross power can become significant, which complicates the scattering analysis of open waveguides. Finally, the generality of the proposed method is discussed through a three-dimensional test case considering an embedded bar with an oblique break.