I mean i need to perform a Fast Fourier Transform (FFT) low pass filtering on a time domain data. I have a data file containing of 100000 data point by 0.01 time interval.
I suggest you have a look at the following Matlab functions:
[b,a] = butter(n,Wn,ftype) This will design a Butterworth filter with the characteristics that you need. A Butterworth filter is designed to have as flat as possible a response in pass band. If you need different characteristics, other functions are avaialable to design different kinds of filters.
y = filtfilt(b,a,x) Once you have your b and a from the previous step, then you can use these to filter your signal x.
Follow the suggestion by Costanzo Di Maria and implement the digital filter directly. If you use filtfilt, as he suggests it avoids issues of phase and delay.
I would suggest you may use FIR1 filter. Which can be implemented using FDAtool in MATLAB very easily. If you still not able to Figure out let me know I can share my code for filtering.