Hi,
If you want to protect your board very nicely
You have transparent boxes that you can order (very cheap ~3$)
Which gives a proffesional look to your project.
See this Video
And what is wrong with clear acrylic? It is DESIGNED for the Arduino.. protects the Arduino, as well as allowing access to the I/O pins for development still.
Taking a random box and trying to retro fit (IMHO) doesnt offer any bonus.