Are you looking to remove the soldermask openings for some pads? If so, you can do this using padstack processor for either specific pads from the list, or previously selected padstacks.
If you need to add an extra area to negate some openings in the soldermask, you could possibly achieve this by adding the graphic as a user layer, then using Mask Generator to add the masks together.
Do you have a picture of what you would like to achieve?
As you noted, I would like to negate some of the openings in the soldermask using a rectangular shape. Mask Generator isn't an option as we don't have that license. I will explore the padstack processor option.