Hi Caroline,
First to all, it always depends on the complexity of your problem. Anyway, in Telemac, going from a 2D to a 3D could be not as difficult as it seems.
Of course, there are a lot of things that you should take into account, even before starting a simulation, e.g. :
i) hydrostatic or non-hydrostatic 3D simulation?
ii) treatment of the boundary conditions (for example, velocity profile at the input...)
iii) turbulence model
iv) etc...
I'd recommend to take a look to the examples. They will give you an overview of the diffent possibilities with increasing complexity.
All the best,
Pablo