Controllogix pulse input for linear sensor?

Hello,

How to configure pulse input on AB Controllogix for linear sensor With start stop pulse.

http://www.balluff.com/balluff/MDE/en/products/catalogue/products_details.jsp?id=BTL00A0-127687

You don't. There is NO way a PLC can detect the time between start and stop pulses accurately. Also, the pulses are so fast the PLC may not detect them anyway. You need to buy a card that has a special interface for start stop MDT rods.
If you just need the interface then get this:
http://amci.com/plc-modules/plcmodules-controllogix-ldt-interface.asp
If you are trying to do motion control then get a 1756-HYD02.
What is the application?

These special interface cards have counters that count over 100Mhz. I think the 1756-HYD02 counts at 120 MHz.