What i would do is put a medium under the deep and put a clearer board between. If you don’t have one then do the same but shake/brush the bees into the medium below, enlisting the help of an assistant to store the empty frames in a box as you take them off.
Cover the box with a lid for a few minutes so that the bees go down (or smoke them) then take your deep away
If the deep is empty and you want the bees out, just set the box on it’s end in front of the hive about a half an hour before dark. By dark they will have moved into the hive mostly. Or just pound them off of the combs. Grasp the end of the frame with a fist and hit that fist with your other fist with a double tap. The 95% of the bees will fall off. When you have pounded them all off, put the box in front of the hive until it’s empty that night.
If your inner cover has an oval hole, then you may want to try one of these bee escapes (known as a Porter escape): http://www.brushymountainbeefarm.com/Bee-Escape/productinfo/776/
I have had a lot of success with the Porter bee escapes in the past, but a lot of people don’t like them. The reasons are that they get propolised shut quite quickly, and if the metal springs bend or move (which happens easily), bees can get around them. You can’t use them with a round hole in the inner cover, though.
As Michael says, shaking is a good method too. In one of @JeffH’s videos, you can see Jeff doing a “triple jerking down-shake” of a frame over the hive (my quotes, not his) and this is a very successful and quick method for me to remove more than 95% of the bees from a frame. It is remarkably atraumatic for the bees - they don’t get annoyed and very few take to the air. They make a lot of noise for a few seconds, but then they quickly get back to work.
