Setting timer3 in CTC mode - conflict with servo library
Unfortunately, The Servo library reserves output compare A (OCR*A) on timers 1,3,4, and 5 when loaded on an arduino mega. Each can only have one ISR, so you will not be able to define your own TIMER*_COMPA_vect while you use Servo without modifying the library. 

However, each hardware timer is equipped with 2 output compare registers. Servo does not claim any TIMER*_COMPB_vect interrupts, so those are free to use, and work exactly the same.

You should watch out for the Servo libraries activities, it could change the configuration of your timer. The default order is on megas is 5,1,3,4 and to give each 12 servos. It only configures the timer once it needs it, so you should be fine using timer 3 until you add that 25th servo.

To change your code, use OCR3B instead of OCR3A (the Output Compare Registers) and set bit OCIE3B instead of OCIE3A in TIMSK3 (the Output Compare Interrupt Enable bits). Then you to change your ISR function to  ISR(TIMER3_COMPB_vect){}

CTC mode only works with OCR3A, but if you set TCNT3 to 0 in your interrupt function you can get similar behavior. Remember to remove the line that turns CTC mode on using WGM12.