Update: Second version is here. I make the holder smaller to provide better grip. Now you may use it to hold your Apple Pencil right away without using any padding. The clip will fit better with the edge of Smart Keyboard, though I still recommend some padding there.
I want to have Apple Pencil attached to my iPad Pro and Smart Keyboard so I can easily carry all of them around, but Apple does not provide any official accessory for holding Apple Pencil with iPad Pro together. I think I would easily lost the Pencil if I have no proper place to place it. So I make my own.
Apply padding to provide better grip
Since the surface of Apple Pencil is very smooth. It is very hard for 3D printing material to grab it firmly without slipping and not not leaving mark on the Pencil, so I got some 1.5mm sponge sheet from stationary shop as shown in the picture below. Cut it into right size and stick it on the inside surface of the clip and holder. Like the second picture below. I've leave enough room for the sponge sheet.