This is a customizeable pen holder that lets you define the number, size and spacing of the holes in a hanging pen holder that clips onto 2cm high shelves from the Container Store
The original design in OpenJSCAD is here and a video showing how I made it.
I've printed this successfully with Rafts and Brims in PLA on Ultimaker, Dremel, FlashForge, and BeeVeryCreative printers.
You don't need to reorient or add any supports for typical sizes.
Putting an adhesive pad like the fuzzy side of a velcro strip on the top clip's underside will help the holder from sliding around on the shelf.