Reset timer on Arduino Due board?

Hi, I just bought an Arduino Due board last week. Now I faced a problem regarding the timer. I can't update the value of the counter. The application is I need a 1000 microseconds timer. When the timer begins, the counter increases from 0 to 1, 2 ... and an interrupt happens when the counter reaches 1000. However, during this process, at some point, I want to reset the timer to 0. The counter register CV is read-only. Can anyone help me?

I think you are misunderstanding how to accomplish your objective. You need to scrap your original plan (meaning forget you ever thought that. really. forget it) and use millis()

http://arduino.cc/en/Reference/millis

Also, take a look at the Blinkwithoutdelay IDE example.

What timer is this? How are you making it trigger an interrupt?