We tried to use a shopbot to cut 1/4" aluminum parts for our climber.
We were actually able to cut it relatively easily with the right bit and feed speeds.
To keep the aluminum fastened down, we predrilled holes in the corners of the aluminum, and woodscrewed it into the bed.
We used the following settings and parts:
a 1/4" carbide flat end mill
10000 RPM
I am unsure of the feed speed we used, but you can figure it out for yourself with this chart:
http://www.bing.com/images/search?q=shopbot+feeds+and+speeds+1%2f4+aluminum+4 +flute&view=detailv2&&id=3D8A69C7291F45AFC372C16BE 10018AA4B57C699&selectedIndex=1&ccid=3ti9%2fpTu&si mid=608004427611244244&thid=OIP.Mded8bdfe94eed06b1 8605e2446230e1fo0&ajaxhist=0
The main problem we ran into was chiploading. We had to pause our machine every so often and remove all of the aluminum chips from the bit, or the bit would start melting instead of cutting, creating rough edges and eventually halting the machine. To remedy this, you might try a slim pass depth.