Unfortunately, the people at Facebook have taken steps to prevent scripts or programs being used to delete your history. No doubt this is because your history is of useful marketing value to them.
The only way to delete the history is to do it manually. Unfortunately, you will have to go in and delete all of the unwanted content by hand. The other option is to block this person which will completely hide all communications between you two. You will not appear on his stuff, he will not appear on your stuff. However, you'll still need to go in and manually delete everything from other people's stuff that you both commented on, and unless you manually delete any content it can still be found by internet search.