Anybody knows about tools in some animation programs like MB which are doing the same that JR doing? just removing this noise?
or some special plugins? Any suggestions will be helpful.

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If you are using Motion Builder, there are filters for animation like Butterworth or several Smooth filters, but why when the JR of iPi works well, maybe if you wanted to use those on top of the JR, but watch using too much, as the animation will lose its realistic look, lesser movement in the action means a bit more JR needed, but use the minimum needed for good appearance and try more Trajectory Smoothing on export.

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