1. Cut the tray out with a dremel or similar (need to be very careful).2. Take the case completely apart to separate the inner case from the outer case and then drill out the rivets.
Neither of those will sound appealing I know, but they are the only practical options.
The other question though is to consider if you might want to keep it. You can make a nice shelf to fix on top of it and run cables (and even water cooling pipes) underneath it. Also, unlike the G5 bottom area - which takes up quite a lot of room to house the PSU - the Mac Pro only has quite a small amount of space at the bottom, so this support is perhaps easier to live with and work around.
This is what I did with mine - I cut the support to allow pipes to run under it from my radiator to the CPU block and I mounted a hot swap base to it so I could use it for extra disk drives.
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