YES there certainly is a way to structure an application in Actionscript 3.0 and it comes in the form of PureMVC.
It is a moderate learning curve but there is a good tutorial on the site for each type of language that PureMVC supports.
You essentially have a facade which is in charge of your application and then a model or multiple models which are represented by mediators which are your view.
If you are serious about creating a good application using best practices, then go and check it out and take time to learn how to use the framework.