Buy 72 pencils (mixed bright colours are fun); measure your pencils across the flats - mine were 6mm. Scale the STL so that the longest distance across the holder (the hexagon diagonal) is 16 times the pencil across-flats distance, so 96mm for this holder (i.e. 16*6mm).
There are two designs of holder, one which is solid, the other which is thinner and can flex a little. It's probably easier to start with the #2 (the springy one); as the solid one can be tight fit to the pencils.
Print 4 holders - one to hold each of the four hexagonal prisms of pencils (18 pencils per prism). Push two of them together at an angle of ~70ÃÂÃÂ° (or arccos(1/3) if you have a calculator & protractor ;-) so that the hexagonal prism edges (are parallel and the pencils touch. Add the next prism so it's also ~70ÃÂÃÂ° from the others. Cross your fingers and push in the last prism.
Elastic bands around the assembled prisms can help keep them in place while assembling.
Discrete drops of superglue will help keep everything together, especially for the pencils along the edges of the prisms.
To help visualise how things go together, I've included a ZIP-ped STL file of the full assembly (72 pencils & 4 holders) which you could view in, say, ReplicatorG.
Note: The holder was drawn up in a CAD package, but I have tried an OpenSCAD version - just not sure if the maths is completely correct.
I'm still tweaking the size of the pencil holes and their separations - if things are too tight, try printing the holder ~5% bigger.
This prints reasonably well on a Makerbot Replicator. (Although the first holders were made of balsa wood with CNC milled holes.)