WordPress already Installed

” To reinstall please clear your old database tables first.”

I have recently done the DIY transfer from WP.COM to WPO.ORG. I was successful in setting up my site however, I wanted to run the new PHP script that I had modified in order to use it with my new WP.ORG blog. But I got the above message. I am not sure how to do that and then reinstall to run my PHP script. Is it even worth doing? ; anyone have any tips on how to resolve this problem?