Timer Interrupt example for Adafruit Feather M0. Callback function can be written in TC3_Handler().

timerInterrupt.ino

#define LED_PIN 13

#define CPU_HZ 48000000
#define TIMER_PRESCALER_DIV 1024

void startTimer(int frequencyHz);
void setTimerFrequency(int frequencyHz);
void TC3_Handler();

bool isLEDOn = false;

void setup() {
  pinMode(LED_PIN, OUTPUT);
  startTimer(10);
}

void loop() {}

void setTimerFrequency(int frequencyHz) {
  int compareValue = (CPU_HZ / (TIMER_PRESCALER_DIV * frequencyHz)) - 1;
  TcCount16* TC = (TcCount16*) TC3;
  // Make sure the count is in a proportional position to where it was
  // to prevent any jitter or disconnect when changing the compare value.
  TC->COUNT.reg = map(TC->COUNT.reg, 0, TC->CC[0].reg, 0, compareValue);
  TC->CC[0].reg = compareValue;
  Serial.println(TC->COUNT.reg);
  Serial.println(TC->CC[0].reg);
  while (TC->STATUS.bit.SYNCBUSY == 1);
}

void startTimer(int frequencyHz) {
  REG_GCLK_CLKCTRL = (uint16_t) (GCLK_CLKCTRL_CLKEN | GCLK_CLKCTRL_GEN_GCLK0 | GCLK_CLKCTRL_ID_TCC2_TC3) ;
  while ( GCLK->STATUS.bit.SYNCBUSY == 1 ); // wait for sync

  TcCount16* TC = (TcCount16*) TC3;

  TC->CTRLA.reg &= ~TC_CTRLA_ENABLE;
  while (TC->STATUS.bit.SYNCBUSY == 1); // wait for sync

  // Use the 16-bit timer
  TC->CTRLA.reg |= TC_CTRLA_MODE_COUNT16;
  while (TC->STATUS.bit.SYNCBUSY == 1); // wait for sync

  // Use match mode so that the timer counter resets when the count matches the compare register
  TC->CTRLA.reg |= TC_CTRLA_WAVEGEN_MFRQ;
  while (TC->STATUS.bit.SYNCBUSY == 1); // wait for sync

  // Set prescaler to 1024
  TC->CTRLA.reg |= TC_CTRLA_PRESCALER_DIV1024;
  while (TC->STATUS.bit.SYNCBUSY == 1); // wait for sync

  setTimerFrequency(frequencyHz);

  // Enable the compare interrupt
  TC->INTENSET.reg = 0;
  TC->INTENSET.bit.MC0 = 1;

  NVIC_EnableIRQ(TC3_IRQn);

  TC->CTRLA.reg |= TC_CTRLA_ENABLE;
  while (TC->STATUS.bit.SYNCBUSY == 1); // wait for sync
}

void TC3_Handler() {
  TcCount16* TC = (TcCount16*) TC3;
  // If this interrupt is due to the compare register matching the timer count
  // we toggle the LED.
  if (TC->INTFLAG.bit.MC0 == 1) {
    TC->INTFLAG.bit.MC0 = 1;
    // Write callback here!!!
    digitalWrite(LED_PIN, isLEDOn);
    isLEDOn = !isLEDOn;
  }
}

TcCount16* TC = (TcCount16*) TC3;
TcCount16* is not declared any where
error mesage comming please explain

Awesome code sample, Sheng. This worked for me on the first try on a Feather M0.
I then adapted it to a different timer rate (200Hz) and that worked too.