Raspberry Pi enthusiast and Thingiverse member Chordless has designed and release the files for a modular Raspberry Pi case enabling you to build a system to your exact requirements.
“A modular case for Raspberry Pi. Print the modules you want, and click them together to make a customized case. This is mostly intended for headless home server or NAS type usage of Raspberry Pi; none of the cases have holes for HDMI cables! Supports pretty much all Raspberry Pi modules you might want to use as a server.
The Pi slides into the case from the top. There are grooves inside the case walls to hold the “flanges” on the usb ports. Make sure these go in the correct place. It’s best if you have M2.5 screws for mounting the Pi. I don’t, so i used M3 screws. I drilled out the holes on the Pi to 3mm, and drilled out the holes on the Pi holder to 2.5mm. Make sure you don’t use screws with large heads; they might make contact with the Pi and short something out.
I recommend using a 12V fan, and using a boost converter to power it. This means we take 5V from the GPIO pins on the Raspberry Pi, “boost” it to maybe 9-10V, and power the fan from this. This will make the fan run slower and more quietly. It’s also possible to run a 5V fan directly from the GPIO pins, but then the fan will be running at full speed = loudly.”
Source: Modular Raspberry Pi case