Starting from Secure Fields 3.0 we give an option to delete a Secure Field history and to not store it at all for the future.
So for instance, when you have a personal information and you are asked to not keep it any longer, you can simply delete the field value and whole history of it.
How to delete history?
It's quite simple. Just go to the issue you wish to delete history for, pick More option and then Clear Field History.
Take under consideration that it will only delete the history, not the current value of the filed. In order to delete everything, delete the current value first and then delete the history.
How to stop storing history?
Also, if for some reason you do want to not store history of a Secure Fields at all, you can set it up, by going to:
Issues → Fields → Custom fields
by the Secure Field you wish to change , then pick
Configure → Edit Permission scheme → unchecking the box Save field history and clicking Done.
And there you go, history for this field will not be kept any longer.