The std under mounted Arduino Mega 2560 (Rev3) with component silkscreen and text added to PCB view.
The USB, and maybe the power connector, will hit any PCB component pin that is mounted directly above it, so I added the Arduino Mega 2560 component positions so you know were to place them. Even if you file the protruding pins flat they will still hit the USB, so it's either avoid those positions or space the headers higher to give the Mega more gap to the PCB.
V1.0 - Arduino Mega 2560 (Rev3).fzpz (86.4 KB)