He is asking how to make some puzzles 3D and others 2D.
Unfortunately, this is an anti-question—how are we supposed to answer? “Just make some 3D and some 2D.”
If you have to ask this it means you don’t have a foundation at all in any form of graphics, 2D or 3D.
Just because most games are entirely 2D or entirely 3D (even then menus will often be 2D) does not mean there is some kind of special game property that restricts it to 2D or to 3D.
If you want something in your game to be 2D—a menu, a HUD, a whole puzzle—do what is necessary for it to be 2D: Use an orthographic projection matrix and a bunch of sprites.
If you want something in your game to be 3D, do what is necessary for it to be 3D: Use a perspective projection matrix and 3D models.
In other words, the answer literally is, “Just do it.”