Using multiple timers and avoiding conflicts I would like to use three timers in CTC mode to launch three Interrupt Service Routines at different frequencies. 

In this application I need to use the servo library, millis() and micros() functions.

Timer3 (Working)

Thanks to this question, Timer3 has been set up in the following way:

  cli();          // disable global interrupts
  TCCR3A = 0;     // set entire TCCR3A register to 0
  TCCR3B = 0;     // same for TCCR3B

  // set compare match register to desired timer count:  @~744 Hz
  OCR3A = 20; 
  // turn on CTC mode:
  TCCR3B |= (1 &lt;&lt; WGM32);
  // Set CS10 and CS12 bits for 1024 prescaler:
  TCCR3B |= (1 &lt;&lt; CS30) | (1 &lt;&lt; CS32);
  // enable timer compare interrupt:
  TIMSK3 |= (1 &lt;&lt; OCIE3B);
  // enable global interrupts:
  sei();

  ISR(TIMER3_COMPB_vect)
  {
     cont++;
  }


Timer4
I've tried with this configuration:

cli();          // disable global interrupts
TCCR4A = 0;     // set entire TCCR3A register to 0
TCCR4B = 0;     // same for TCCR3B

// set compare match register to desired timer count: @ ~744 Hz
OCR4A = 20; 
// turn on CTC mode:
TCCR4B |= (1 &lt;&lt; WGM42);
// Set CS10 and CS12 bits for 1024 prescaler:
TCCR4B |= (1 &lt;&lt; CS40) | (1 &lt;&lt; CS42);
// enable timer compare interrupt:
TIMSK4 |= (1 &lt;&lt; OCIE4B);
//TIMSK4 |= (1 &lt;&lt; OCIE4A); same issue
// enable global interrupts:
sei();

ISR(TIMER4_COMPB_vect) //TIMER4_COMPA_vect same issue
{
  cont++;
}


But the compiler returns an error caused by the servo library conflict:


  Servo\Servo.cpp.o: In function '__vector_42': C:\Program Files
  (x86)\Arduino\libraries\Servo/Servo.cpp:117: multiple definition of
  '__vector_42' Timer4B_800Hz.cpp.o:C:\Program Files
  (x86)\Arduino/Timer4B_800Hz.ino:49: first defined here c:/program
  files
  (x86)/arduino/hardware/tools/avr/bin/../lib/gcc/avr/4.3.2/../../../../avr/bin/ld.exe:
  Disabling relaxation: it will not work with multiple definitions


As Gerben suggested in a comment in this question:


  They are just hogging all timers. I guess you have to alter the
  library slightly by removing the #define _useTimer3 line, or try
  putting a #undef _useTimer3 right after the include. –  Gerben


I would avoid changing the servo library since motors play a critcal role in the application.

Timer 5 Same issue

Which timers and output compare registers can I use to set up the three ISR correctly?
The problem is the Servo library. This library is claiming all the timers, so you can't use them yourself. What I do to fix this is edit the Servo.h (or ServoTimers.h) file. 

#if defined(__AVR_ATmega1280__) || defined(__AVR_ATmega2560__)
//#define _useTimer5
#define _useTimer1
#define _useTimer3
//#define _useTimer4
//typedef enum { _timer5, _timer1, _timer3, _timer4, _Nbr_16timers }   timer16_Sequence_t;
typedef enum { _timer1, _timer3, _Nbr_16timers } timer16_Sequence_t;


This will remove the 2 timers (4 and 5) for the Mega boards, but you can still attach 24 servo's. If you need more, you should edit this file again.