Arduino Due ( Atmel Microcontroller) IC Heat up and led goes off I was connecting L293d Motor Driver IC with an Arduino Due Board. May be due to wrong connections, but when I made the grounds common, the Arduino LED goes off and Atmel IC heats up. When I reconnect my Due board with my PC anytime, the LED turns on and slowly dims to off and Atmel IC fries up.

I wanted to repair it. What should I do? 

I have checked the input voltage of the AMS1117 3.3V regular IC as 3.8 V, while the output is 2.2 V. If I externally give 5 volt at input again, the input voltages drops. The regulator is loading.

I thought of replacing the regular IC?
Will that work?

Also I externally powered the Board with 3.3V by its pin labeled "3.3V" . The LEDs glow on and did not go off. But the Atmel Microcontroller IC becomes very hot.

What should I do?
Motor driver boards exist to allow an MCU to control a motor without having to supply its power. If you try to power motors from the Arduino as well, they draw too much current and things get hot or damaged.

The 3.3v pin is only for supplying modest amounts of current at 3.3v from a 5v Arduino. You can not back-power the board with it. I don't know what happens if you try, but I bet it isn't good...