Hello,
If you can work with the code and matlab, I'd recommend you first try POSTEL3D. It is one of the TELEMAC modules to build 2D cross-section files (vertical and horizontal) from your 3D SELAFIN file.
POSTEL3D create 2D SELAFIN files (for horizontal slices) of 2D LEONARD files (for vertical slices). You shoul dbe able to load these both in Matlab. Do have a look at the POSTEL3D manual.
Final note: there is also an existing Matlab tool developed by HR Wallingford for TELEMAC applications, available here:
Mermaid
Hope this helps.
Sébastien.