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Forgive me if I sound stupid, but could someone explain to me the workflow of capturing my Mocap data within ARENA and then taking it in to Maya to apply it to my character. I do not actually own the optitrack system yet. For now I just want to know how it works. I know that you can save your data as bvh but how exactly would I use it? Thank you for your time.

Once you capture the data(motion). You can edit the capture itself, then export it as a BVH file; which you then import into your 3d software(maya), and attach the data points to a 3d skeleton model.