Please give more precise details, it is very difficult to answer a question with an extremly limited amount of information to go on. "Detailed questions get detailed answers"
Firstly what 3d application are you using?
Secondaly I presume its for compositing into AE?
In that case depending on the 3d application usually two ways:
(1) Use render object ID (render elements) if your 3d application supports this.
(2) Select the background colour to something like green, then just do a chromakey on the rendered footage.
Ok, now that the question is much clearer now, I know there are many here that are very well versed on C4D and should be able you tell you how to render seperate elements/ isolated objects.
If it does not have that option in C4D then you can always render with a "greenscreen" background and key it out.