If you want to delete the database records you'll need to manually within phpMYAdmin.
1. Backup your database first in case you make any errors.
2. Select your main database
3. click on wp_blogs table and it will open
4. Select blogs you want to delete and individually or tick the box on the far right and delete from the bottom option. You'll be given a screen to OK the action or cancel.
I'm sure you wanted to know how to do it automatically. Sorry, I don't know of any.
You may want to clear your "overhead" which is the far right column while you doing database maintenance.
1. With the main database selected selected all table from the bottom left side of the tables list.
2. Select "Optimize table" from the drop down.
Wait for it to finish then check tables and see there all there and you didn't select delete instead of Optimize. LOL I admit I did that once while in a hurry.
Remember fist step, BACK UP DATABASE