You can definately petition the Court for a Civil Protection Order. I am attaching a copy of the instructions for filing a Civil Protection Order from the Hamilton County Clerk of Courts website for your review. Here's also a copy of the actual paperwork you'll need to file: http://www.courtclerk.org/forms/StalkingProtectionOrder10-03D.pdf
The process first begins with an ex parte hearing (hearing in which only you appear). If the court is conviced based on your application that a civil protection order is permissible and warranted given the law and the facts, it will issue an ex parte temporary order. This order is typically only good for fourteen days. You'll then have to return in about two weeks for a full hearing in which your stepdaughter's mother can appear. Both sides present testimony and evidence as to why a permanent order should or should not be issued.
Just because your spouse's ex has visitation or custodial rights to your stepdaughter does not mean she has a legal right to come to the house to harass, stalk, and assault you. Talk to your spouse about making arrangements to do transfers of custody after visitations at some place other than where you'll be. You can do that even without a restraining order. And if one is granted, that's what will have to happen in order for her to see your stepdaughter anyways.
I'd consult an attorney about filing out the paperwork and getting the necessary witnesses and evidence ready for a full hearing to maximize your chances of success. Good luck!
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