You should be able to copy the library from you canvas-fla to an empty as3 fla
Copy-pasting of stage-objects, library-items, timeline layers and frames etc., all work across different doc-types in Flash Pro just like before. So, you shouldn't have any problems in reusing your contents in a different doc-type. When you copy-paste something that is not supported in the current doc-type, you get a warning message about that as well.
An easy way to achieve what you want would be:
1. Select all the timeline-layers in your current document.
2. Right Click -> 'Copy Layers'
3. Goto your new document, Right click on the timeline-layer -> 'Paste Layers'.