One thing that is currently missing from the Apollo Filesystem-API is the ability to get a native save file dialog.
It`s easy to create a file open dialog with the open()-Method of the File Object. So until the File Object gets a save() method i use the download()-Method.
The File class extends FileReference and so inherits its download()-Method. The problem is that the download Method takes a URLRequest Object as a parameter.
So after the OPEN event make sure to cancel the download request with file.cancel(). Now you can access the url via the normal File attributes.
Here is some example code:

private function saveFile():void
{
file=new File();
file.download(new URLRequest(“http://www.nourl.de”),”exported.swf”);
file.addEventListener(Event.OPEN,swfSavePathSelected);
file.addEventListener(IOErrorEvent.IO_ERROR,savePathSelected);
}

private function savePathSelected(evt:Event) : void
{
file.cancel();
fileStream = new FileStream();
fileStream.openAsync(file, FileMode.WRITE);
fileStream.writeBytes(b);
fileStream.close()
}

This worked great for me in earlier projects. At some point i got some errors which seem to be related to the nonexisting url and the app would just hang. In order to avoid this
i did an quich and ugly hack. I also added an event listener for the IO_ERROR event and did all the saving stuff their. Not nice but temporarily fixed it. I got confirmation that
the missing save()-method will be somehow implemented in later builds, so i can live with this hack in the meantime.
Anyone got a better solution?

UPDATE:
Found this post by Robots w/Lasers that has more about this