Hello Sina,
If your initial mesh is expressed in longitude/latitude and you want your results in the same coordinates, you have to keep the keyword RESULT FILE IN LONGITUDE-LATITUDE at its default value (= YES), otherwise with your set-up, it will be written in Mercator projection.
Do I have to understand that you try to visualise the 3D mesh in the pictures? I have not read any answer to one of my previous question.
You may have to use double precision for your coordinatesin longitude/latitude.
In TELEMAC-3D, it is managed with the keyword GEOMETRY FILE FORMAT. Then you have to choose SERAFIND (with a D as double precision) or MED.
Hope this helps,
Chi-Tuan