This assumes that 1: you can reliably measure at that small of a time difference and 2: you can submit enough requests without being detected.
If you're wondering, "how do I detect nanosecond differences over a network when my measurement will be swamped by other things happening on the target, the network, and my host", the answers boil down to:
* You're going to move your measurement code as close to the drivers as possible, and fix interrupt handling so that interrupts don't confound your measurements.
* You're going to get yourself on the same hosting provider as your target; for instance, a good chunk of all target apps can be attacked via Amazon EC2 for not very much money.
* You're going to take lots and lots and lots and lots of measurements and then use high school statistics to process the results.