sTrider_7:
I want to remove the Arduino bootloader on my mega board so that I can write standard AVR C code and upload it through the USB connection.
Arduino IDE puts the compiled hex file in a directory like this:
C:\Users\Victor\AppData\Local\Temp\build1325897986179133197.tmp\Blink.cpp.hex
You have to remove that "Blink.cpp.hex" from there and replace it with the code compiled by you using another IDE, ex. Avr Studio, and then load the program into your Arduino Mega using Arduino IDE.