Hello Kian Chong,
I would suggest to use a buffered-period example with the counter on the 6034E and use the 1 PPS signal as the gating signal.
When you configure a counter for a buffered-period operation, the counter will latch the data from hardware on the edge of the gating signal and will also reset the counter back to zero. So you could use the 100 kHz timebase as the source and the 1 PPS signal as the gate.
The Measure Buffered Period (DAQ-STC) VI shipping example within LabVIEW will do this for you.
Regards,
Todd D.
NI Applications Engineer