I want to make Arduino Mega 2560 board. As the reference files are given on Arduino Site, I don't want to add USB communication on the board. So can I remove part of ATMega 16? Will it cause any kind of problem in working of board? And if It will fine to remove ATMega 16 part, How much part of schematic to be change?
Yes, you can omit the ATmega16U2 and its accompanying parts. That is, the whole right block of schematic in this sheet.
The resulting board will work perfectly fine, it will simply no longer have a built-in programming interface, nor a built-in USB-serial interface. You will likely want to buy an FTDI cable and an AVR programmer, if you do not already have these.