Boolean difference not carving correctly After applying a boolean modifier there is no surface on the area that was carved by the cylinder. It's kind of hard to explain in words. I have a before and after picture. In the after you can see there is no surface on the first part of the hole that was created. Wondering what is causing this...

before


after
you could try the following:
Go into edit mode, press a to select all, then w and remove doubles
now back into edit mode, press ctrl+a and apply the rotation and scale.
now try the boolean modifier again

are there any other things in your modifier stack ?