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Yes, you most definitely can do structural changes to the home, infact, you can do pretty much anything you want to the home short of completely replacing the foundation.
Your loan officer should be able to guide you through this process, if they can't then they're inexperienced in doing these and you should find a new one.
Your HUD consultant will let you know if there's anything you can't do or isn't feasible for your future home. Make sure to be nice to them because they'll be the most helpful person aside from your loan officer during one of these loans.