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You can import .c3d file in blender like this:

http://stackoverflow.com/questions/20499320/how-to-import-c3d-files-into-blender

The problem is it won't be an armature, but animated locations of points:

Some points will be dead in the center (marked).

1. Clean up the mocap - delete the dead markers
2. Recreate the armature to fit the points
3. Constrain the bones with Copy_Location(only for roots) and Track_To/Dumped track constraints to follow the points. You might need couple of these constraints to first track some point to lock bone Y rotation and then track another point for the bone direction.
4. Bake the animation into an Action with Pose > Animation > Bake Action: visual_keying_ON, clear_constraints_ON
5. Export the armature as a .bvh (you might need to enable BVH addon)