Hi
I would like to know if there is any way I can bootload the ATmega16u2 in my Mega 2560 R3 board with an Arduino Uno ?
It's exactly the same procedure as you would install a bootloader on the ATmega2560, just using the other ICSP socket (you probably have to solder a connector on it). If "bootload" means just installing a new firmware on the ATmega16U2, you can do that by DFU (http://arduino.cc/en/Hacking/DFUProgramming8U2).