SerialTest.pde

// We'll use timers 3 and 4
HardwareTimer timer3(3);
HardwareTimer timer4(4);

void setup() {


  // Pause the timer while we're configuring it
  timer3.pause();
  timer4.pause();

  // Set up period
  timer3.setPeriod(1000); // in microseconds
  timer4.setPeriod(90); // in microseconds


  timer3.setMode(TIMER_CH1, TIMER_OUTPUT_COMPARE);
  timer4.setMode(TIMER_CH1, TIMER_OUTPUT_COMPARE);
  timer3.setChannel1Mode(TIMER_OUTPUT_COMPARE);
  timer4.setChannel1Mode(TIMER_OUTPUT_COMPARE);


  timer3.setCount(0);
  timer4.setCount(0);
  timer3.setOverflow(3.,000);
  timer4.setOverflow(30000);

  timer3.setCompare(TIMER_CH1, 1000);   // somewhere in the middle
  timer4.setCompare(TIMER_CH1, 1000);

  timer3.attachCompare1Interrupt(handler3);
  timer4.attachCompare1Interrupt(handler4);

  // Refresh the timer's count, prescale, and overflow
  timer3.refresh();
  timer3.refresh();

  // Start the timer counting
  timer3.resume();
  timer4.resume();
}

void loop() {

}

void handler3(void) {
  SerialUSB.println("Teste 1");
}

void handler4(void) {
  SerialUSB.println("Teste 2");
}

com base nos exemplos de: http://leaflabs.com/docs/lang/api/hardwaretimer.html#using-timer-interrupts