If you don't feel comfortable with your stbxw in your house then, unless there's an emergency, she should not be in your house.
A few weeks after separation, I told my wife that she wasn't welcome in my house. She could come to the front door, but that's as far she could go. There were several reasons for doing that; the main reason was that we'd usually begin arguing when she'd come into the house and I didn't want that to continue.
To enforce that, you have to be willing to call the police if she comes into the house and won't leave when you tell her to go. (The cops handle those types of situations all the time; it's not a big deal to call them.) It also helps to change the locks and get an inexpensive video camera to monitor the door.
