From the FAQ:
How to get rid of that "orange marker" that indicates my uboat position?
Simply delete the associated graphics file. It is located at "Program Files\Ubisoft\SilentHunterIII\data\Misc\UMark.tga" . Be sure to make a backup first, or simply rename the file.
Or hit CTRL+DEL. This removes the orange indicator while being submerged.
http://www.subsim.com/phpBB/viewtopic.php?t=28146
Matbe this is what you are looking for. Not sure i understand what you mean by the "3d map".