Integral representations for the solution of the Laplace, modified Helmholtz, and Helmholtz equations can be obtained using Green's theorem. However, these representations involve both the Dirichlet and the Neumann values on the boundary, and for a well-posed boundary value problem (BVP) one of these functions is unknown. A new transform method for solving BVPs for linear and integrable nonlinear partial differential equations (PDEs), usually referred to as the unified transform or the Fokas method, was introduced in the late 1990s. For linear elliptic PDEs in two dimensions, this method first, by employing two algebraic equations formulated in the Fourier plane, provides an elegant approach for determining the Dirichlet to Neumann map, i.e., for constructing the unknown boundary values in terms of the given boundary data. Second, this method constructs novel integral representations of the solution in terms of integrals formulated in the complex Fourier plane. In the present paper, we extend this novel approach to the case of the Laplace, modified Helmholtz, and Helmholtz equations, formulated in a three-dimensional cylindrical domain with a polygonal cross-section.