Using harware Timer

I am using Arduino SDK for Linkit one programming.
I have gone through the software timer ex. in advanced digital i/o.
duration = pulseIn(BUTTON, HIGH, 1000000L);
it gives me time duration between two pulses.
But using this code gives limitation in multitasking.

Hence I wanted to use Hardware timer. where external clock frequency will be output of sensor.
I want to initialize the timer in beginning, and can check the no of pulse occurred after certain duration.

Please help me out.