How would you make a group selection that only selects what you want in the 3rd dimension? Selecting on a desktop or in games like factorio is easy, because there are only 2 dimensions which your mouse can handle easily.
Two ideas for this:
1) Quick and dirty, a second deletion mode that removes the time required to delete, so that "on click" my target is removed (instead of having to hold for a second) - mouse click spam macros would do the rest for heavy deletions.
2) you can select a foundation and span a 2d rectangle along the height of this foundation. In the end, you select only connected foundations that have the same height. Once you release the button, all the selected foundations and everything build on top of them gets removed (everything standing on them) until another "foundation height" is reached, to ensure you only delete one floor of a multi floor building.
Technically this would be something like "get all entities within the selected length and width and sort them by height coordinate. Iterate through the list and remove until a foundation is reached that does not have the initial height coordinate."