To design your pen you can use any 3D modeling software. Inventor is the most ideal software if available to the school your at. Its free to schools and you can download a version of it here if you don't have one already. In the Tutorial page of the website you can find video tools on who to use Inventor.
Another great option is Google Sketch up. You can download a plugin to convert sketch up files into .STL files which are 3D printable. Many schools that are one to one have chosen to use APPLE products and you can download a MAC version of Google Sketch up. It is one of the only programs that is comparable with MAC to create STL files. Download Sketch up for free here.
step two
After you have created the pen you can convert it to an .STL file and print each part. The prints take about on hour per pen. This is a quick project that is inexpensive for students to create and take home with them.
purchase parts
The parts I use for this project are from Penn state industries. They are made fro wood turning however if you measure the parts correctly they were perfect for replace the wood turned parts with 3D printed parts. They are assembled the same way and cost is minimal. Purchase pen kits here.