Have not got it in front of me but first step is check the initial hex for the DS* at the start of the file to see if it matches one of the known formats (NSBMD being a common one but not the only one). Not all detection in the likes of tinke and crystaltile2 is that accurate and extensions are not really a thing the DS pays attention to.
*for something without a file, or if the DS game decides to stuff the model in a binary/overlay then you first need to find the file/code responsible however you will.
If it is truly an unknown custom format made specifically for the game then you get to reverse engineer that. The DS is rather weak so most formats don't experience radical changes between being in the ROM and being on the screen. To that end description of the DS 3d hardware http://problemkaputt.de/gbatek.htm#ds3dvideo
Personally I like to try to find the basic shapes first if I can in the game (sometimes you will get a nice flat cuboid made to put a texture on, spheres are used somewhat often in things too) so I can at least get some grasp of things there. Others though will follow it from the file until it lands in 3d hardware and thus know what each part does.
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