It's easy to delete an instance that uses the root store -- just terminate it.
But how do I delete an instance backed by EBS? My terminated instances are just sitting there.
In order to terminate an EBS rooted instance you need to both terminate the instance and also remove the EBS storage, although that'll make the instance not recoverable of course.
Every time a new EBS instance is spawn a copy of the initial snapshot is spawn into an EBS volume which will be used as root for that instance.
I think that's pretty much all that is needed, I never had to remove one myself so let me know how it goes!