A few pins of atmega16 (D0,D1,D2) are always high when uC is powered.Does it mean those pins are damaged ??
Or is there a way to reset those pins to low ?
** I have tried programming the output of those pins
Does the chip have a bootloader installed? If so, it might enable UART before main() starts. Explicitly disable subsystems you don't need. This also helps battery life if applicable. Also see the PRR register which is often overlooked.