You're asking multiple of questions none of them are easy enough to explain in a Q&A, you'll have to do your own research into the subjects and ask about the bits and pieces that troubles you.
About storing your 3D objects in an array, I'm guessing you know how to take an object and put into an array, so I believe you mean to ask how you can access your 3D objects, but that's hard to say without knowing how they are create and where they are placed. If they are defined in your XAML you can either set the Name property so you can use them in your code behind or iterate over the children of the panel containing your 3D objects.
To get you started with your research into transformation and animation here are two CP articles
WPF Tutorial - Part 1 : Transformations[
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WPF Tutorial - Styles, Triggers & Animation[
^] - The animation part explains the basics of storyboards(animation) quite well and to the point.