If I understand correctly you just want to create a new data set without any transactions, but with all of your added accounts, categories, reminders, reports, etc.
I don't think there is a canned way of doing that because it might be easier to just create a new file and add back all your accounts and customization.
But if I wanted to do the same. I would just create a new file and use the Import Backup feature to restore a copy of the old data set to the new file name. Then I would access each account one at a time, select all the transactions, and delete.
Then you will have a new data set file name, with all your old stuff and no transactions. You may have to do a bit of cleaning, but I think you can do it.
Like I said, it may be easier, cleaner, and happier for MD just to create the new file and create all the accounts and categories from scratch.