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use MovieClips to make that happen. Think of the MovieClip (MC) as a smaller timeline animation that resides within the main timeline.
Because that's exactly what it is.
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layers don't exist in your published file so you can't control individual layers.
to work-around that follow the advice of rezun8 and convert each layer to a movieclip. ie, select all the frame in that layer, right click > click cut and then create a new movieclip and paste the cut frames into the new movieclip's timeline.
you can then control that movieclip's timeline independent of the main timeline.
thanks a lot for explanation!