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I am working with Atmega128 and i want to write a program that enters the boot section when a particular pin is low and after executing boot program looks in the application area of Atmega128. If some program is present there i want to erase it. Up till noe i have managed to cause the program to enter in boot section and execute the code. But further i have no idea how can it make a search for the presence of some code in application area and then to erase it. Thanks in advance.
Your problem is probably because you have spent too much time reading 8051 or maybe ARM datasheets.
Start by reading the documentation for the ATmega128. If that isn't enough, then try visiting a forum that is discussing the Atmel AVR chips. One suggestion is the AVRFreaks site.