Acoustic or electro-magnetic scattering in a waveguide with  varying direction and cross-section can, if the variations takes  place in only one dimension at a time be re-formulated as a  two-dimensional scattering problem. By using the so-called  Building Block Method, it is possible to construct the  scattering properties of a combination of scatterers when the  properties of each scatterer are known. Hence, variations in the  waveguide geometry or in the boundary conditions can be treated   one at a time.  We consider in this work acoustic scattering, but the same  techniques can be used for both electro-magnetic and some quantum  scattering problems.  By suppressing the time dependence and by using the Building Block  Method, the problem takes the form of the Helmholtz equation in a  waveguide of infinite length and with smoothly varying geometry and  boundary conditions.  A conformal mapping is used to transform the  problem into a corresponding problem in a straight horizontal  channel, and by expanding the field in Fourier trigonometric series,  the problem can be reformulated as an infinite-dimensional ordinary  differential equation. From this, numerically solvable differential  equations for the reflection and transmission operators are  derived.  To be applicable in the Building Block Method, the numerical  conformal mapping must be constructed such that the direction of the  boundary curve can be controlled. At the channel ends, it is an  indispensable requirement, that the two boundary curves are (at least)  asymptotically parallel and straight. Furthermore, to achieve  bounded operators in the differential equations, the boundary curves  must satisfy different regularity conditions, depending on the  properties of the boundary.  Several methods to accomplish such conformal mappings are  presented. The Schwarz-Christoffel mapping, which is a natural starting point and for which  also efficient numerical software exists, can be modified in  different ways to round the polygon corners, and we show algorithms  by which the parameter problem can be solved after such  modifications. It is also possible to use the unmodified Schwarz-Christoffel mapping for  regions with smooth boundary, by constructing an appropriate outer  polygon to the considered region.  Finally, we show how a so-called  zipper algorithm can be used for waveguides.