AVR-Chat

I am setting up a timer. I am trying to measure milliseconds. I have 
set the output compare on timer 1 (prescale of 1) to 16000. 

I get the interrupt triggered, and I am able to increment the 
millisecond counter. Does the timer's counter get reset to zero 
automatically and immediately? I suppose it does not. What do I do to 
force it to reset? 

Do I write zero to the counter? Doesn't the timer lose a few ticks in 
this process? 

I did not notice a setting to cause the timer to reset automatically 
when the outputcompare interrupt is triggered, but I would have 
thought one exists. 

-Tony