Flatter Cookies?

I can't remember which blog I learned this trick from,  immediately after removing a tray of cookies from the oven, gently run a fondant smoother over the entire batch of hot cookies,  and don't remove them from the tray until they're mostly cooled. They'll end up perfectly flat and smooth.

Can you post a picture of your cookies, and perhaps your recipe, so I can better see what the trouble is? Also describe how and when you roll you dough (before or after chilling)? You really shouldn't have to run a fondant smoother over cookies if the recipe is sound and the dough was well chilled and rolled evenly to begin with. I'm thinking you are doing something less than ideal in the upstream process that could easily be corrected.

I chill the dough before cutting, of course, then chill again after cutting.  If there are any bubbles when they come out of the oven, I immediately just flatten them gently with my fingers.  Then they cool in the pan for about 10 minutes before I remove to cooling rack, and I always bake on parchment.