This case fits an Arduino Mega (held in with double-sided foam tape), plus a low-profile proto shield. There is space to hold a 9 volt battery for portable operation. I designed this case for a project that produces an audio output. Therefore the case also includes a hole for a panel mount 3.5mm headphone jack between the USB and power connections on the Mega.
The top panel snaps into the case for protecting your project, but is not required.
I have uploaded the FreeCAD file so that you may modify the case and panel to suit your needs.