The Arduino bootloader burning process takes care of erasing the chip and setting the fuses.
If the chip fuses have been set to require an external crystal or resonator you will need to provide the crystal or an external clock.
If the chip fuses have been set to disable either the serial programming or the Reset features you will need a High Voltage Parallel Programmer (like the High Voltage Rescue Shield) to reset the chip to factory settings.
What ISP device are you using to program bootloaders?