Shortening machine screws and bolts is a sore task, especially fastening them securely in a vise. This very simple, cheap and customizable thingy can ease the burden :) As a bonus, measuring the desired length and filing is also a lot easier. It is a simple design but it works great.

You need two of them to make it work. I advice a lower and a higher cube to make the fastening easier (see pictures and STL's). For each piece you need a fitting nut.
It is customizable but STL's for M3, M4, M5 and M6 are included.

As a second bonus you can use them as calibration cubes and use them afterwards (measurements of STL's in filename).

Tips:

• Make the nut-size a little smaller for a tight fit (customizer)
• Don't make the threadhole too narrow (customizer), strength comes from nut.
• Print them with 4 or 5 walls, top and bottom. PLA works fine.
• You can use leftover filament, these are small prints.
• Press the nut in with your vise, use a screwed in bolt to press them just a little more.
• If the nut is too loose, use some glue. Too tight, heat up the nut and press it in.

Happy shortening :)

PS. It works in the Thingiverse Customizer. If it has a bad day, you can always use OpenScad, it is free and has a built-in customizer.

Look for more tools and the like here:
https://www.thingiverse.com/Coat/collections/coats-toolbox

More information about the fantastic and challenging program OpenScad can be found here: https://en.wikibooks.org/wiki/OpenSCAD_User_Manual