Hello,
If the vertical "walls" of your channel are on the boundary of your model, such as a flume, then you do not need to worry. Just use the bottom bathymetry for your model. TELEMAC will treat the boundary-edge of your model as vertical wall, while allowing the free surface free to move up and down. You can even add boundary wall friction. That is usually how one models bridge piers, vertical hydraulics structures, etc.
However, if your vertical walls / channels are within a bigger area mapped by a TELEMAC unstructured mesh then by definition, your mesh will not allow for two points to be placed one above the other. We are currently developping new algorithms in TELEMAC-3D to allow you to have that capability. This is likely to appear with v6p3 next year. But in the meantime, we recommend you just use a very steep slope (with enough node refinment on it and around it) to represent your "vertical wall" in 2D or 3D.
I hope this helps.
Sébastien.