Wave reflection and transmission characteristics in waveguides are an important issue in many engineering applications. A combined spectral element and finite element (SE/FE) method is used to investigate the effects of local non-uniformities but limited at relatively low frequencies because the SE is formulated by using a beam theory. For higher frequency applications, a method named a combined spectral super element and finite element (SSE/FE) method was presented recently, replacing spectral elements with spectral super elements. This SSE/FE approach requires a long computing time due to the coupling of SSE and FE matrices. If a local non-uniformity has a uniform cross-section along its short length, the FE part could be further replaced by SSE, which improves performance of the combined SSE/FE method in terms of the modeling effort and computing time. In this paper SSEs are combined to investigate the characteristics of waves propagating along waveguides possessing geometric non-uniformities. Two models are regarded: a rail with a local defect and a periodically ribbed plate. In the case of the rail example, firstly, the results predicted by a combined SSE/FE method are compared with those from the combined SSEs in order to justify that the combined SSEs work properly. Then the SSEs are applied to a ribbed plate which has periodically repeated non-uniformities along its length. For the ribbed plate, the propagation characteristics are investigated in terms of the propagation constant.