#include <stdint.h>
#include <avr/io.h>
#include <avr/interrupt.h>

volatile uint16_t ctr;

ISR(TIMER1_OVF_vect)
{
  ctr--;
}
...
int
main(void)
{
   ...
   ctr = 0x0200;
   start_timer();
   while(ctr != 0)
     // wait
       ;
   ...
}