You didn't mention processor type.
On PSoC4 and PSoC5 you can use a custom component StopWatch to measure elapsed CPU clocks
And for PSoC6
Thanks for the reply.
I'm using a PSOC5LP.
I'll take a look at using the stopwatch.
I'm hoping to the be able to get nanosecond resolution.
The StopWatch accuracy is 1 BUS_CLK, which at 80MHz translates into 12.5ns.