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I'm learning Blender because I want to be able to make simple assets for my Unity3D projects. For example, let's say I want to design a simple level (labyrinth-like) but with some premade lamps and different tiles on the floor. So i have a few objects in the scene, each with a different material.

I'm a total newbie when it comes to baking. I guess, that what I need is a combined bake. I know how to bake a simple single object with one material: I need to unwrap it, create an image texture in the node editor, set it to a new image and then click "bake".

But when I want to bake this whole "level" that I want to be a single object in the game (so I'll need to export it in OBJ or sth similar), what should I do? Should I Ctrl+J all the things to merge them into one object and then unwrap it and do the usual stuff? Won't it mess up my materials?

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Use the 'Texture Atlas' addon. It comes with Blender 2.7 or higher and can be enabled in the preference panel.

Once enabled, you can access it from the Render Panel:

enter image description here

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