How do I update the content of a field type in the onAfterElementSave() method?
This will return the content for the specific element instance you're on:

$this-&gt;element-&gt;getContent()


And from there you can do your additional content processing.

When you're ready so save it, you can call:

craft()-&gt;content-&gt;saveContent($this-&gt;element);


There are several examples in craft/app/fieldtypes folder where Craft's native field types do additional processing like this.