The UC3-C2 Xplained has 3 LEDs mounted onboard, which are connected to the AT32UC3C2512. These are 3 standard yellow LEDs and all of them are active low.
LED0 & LED1 are shared with Qtouch sensor output. When pressing the Qtouch button (TK0 or TK1), the LEDs are switched on even though the AT32UC3C2512 tries to turn the LEDs off.
LED2 is shared with the micro switch button. When turning the LED on, set the IO pin to output low. When turning the LED off, set the IO pin as input with pull-up. The protection circuitry added to the button will make the LED shine brighter when the button is pressed and the LED is turned on. When the LED is off, any button press will light up the LED.
One dual LED is mounted near the USB connector. It has one green LED which is used to indicate power and one red LED can be used for other purposes. The green LED will be active when power is applied to the board but it can be disable by software form the AT32UC3C2512 device if needed. The red LED is active low and the green LED is active high.