An analytic mode-matching method suitable for the solution of problems involving scattering in three-dimensional waveguides with flexible walls is presented. Prerequisite to the development of such methods is knowledge of closed form analytic expressions for the natural fluid-structure coupled waveforms that propagate in each duct section and the corresponding orthogonality relations. In this article recent theory [Lawrie, Proc. R. Soc. A. 465, 2347Soc. A. 465, -2367Soc. A. 465, (2009] is extended to construct the non-separable eigenfunctions for acoustic propagation in a three-dimensional rectangular duct with four flexible walls.For the special case in which the duct cross-section is square, the symmetrical nature of the eigenfunctions enables the eigenmodes for a right-angled, isosceles triangular duct with flexible hypotenuse to be deduced. The partial orthogonality relation together with other important properties of the triangular modes are discussed. A mode-matching solution to the scattering of a fluid-structure coupled wave at the junction of two identical semi-infinite ducts of triangular cross-section is demonstrated for two different sets of "junction" conditions.