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I am programming a software which I am developing at the moment, to the PIC18f46K80 by TNM 2000 universal programming. When I read back the PIC, I see that the EEPROM has been written some data. This data is which my software writes to the EEPROM under some conditions. I want the EEPROM to be completely clear when I first program the mcu. I have never seen or realized that a programmer to write to eeprom while loading the software to the pic. Do you have any ideas about why this happen? Thanks.

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Welcome to Stackoverflow! Can you please elaborate your question having your effort like code or something so that people could get your problem early and help you? Thanks!Enamul Hassan
I only wonder when I program the microcontroller, shouldnt the eeprom be clear? I am erasing the mcu before programming, and when I erase it, I check the EEPROM, and it is clear. After I program, I read again, the eeprom is changed.Yusuf

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Assuming you are using MPLAB X for PIC programming, there should be a "Preserve EEPROM Memory" checkbox in your PICkit configuration.

Make sure its not ticked.

Additionally, you may select the "EEPROM" checkbox to make sure the EEPROM gets erased.