I tried to remove the ATMEGA2560 of the Arduino board to use in another project.
Do you mean "off of the Arduino board", like de-soldered it?
Hex generated in atmel studio works perfectly
So the hex works in the Atmel Studio Simulator?
Two things :
1)Is there any chance you overheated the cheap in removal?
2)You might want to try something like AVR-dude and check this out :
http://shannonstrutz.com/?p=629