The 3D cutscenes were pre-rendered, that means you'll need a 3D modelling program to make the 3D models, texture them and then animate them and render them all in that style.
Now as for MI like game engines, there's very little chance you'll get hold of the engine they use, they keep those sort of things to themselves unless a company comes along offering them money (Though some people like Valve like the modding community and offer their engine up)
All I can really say is, buy Dark Basic or Dark Basic Pro, learn how to use it, learn to 3D model, animate and render, load some models into DBP and build yourself an engine that works in a quite similar way.
Dark Basic is fairly easy to understand, you just need to work through it and learn it before you can really do anything. You'll have a lot of features to use to make your 3D engine. At least if you get stuck or have any questions, there's a community here to offer you help and advice.
As for 3D game creators, they are very few in number and often their features are very limited.
Good luck and wilkommen!
Hakuna Matata
