Which data should I use to take the fast Fourier transform (FFT) to find time period for eclipsing binaries? I am trying to use Kepler Data for Eclipsing Binaries to estimate time period, and then other parameters such as mass, eccentricity, semi-major axis, distance, etc. of the system. I want to write code in MATLAB which will use FFT. The available data has the following columns:

bjd(date) | phase | raw_flux | raw_err | corr_flux | corr_err | dtr_flux | dtr_err

Does the data require any cleaning?
If I want to take the FFT of the data to find time period, which data should I use?
For this, you should create a lightcurve, a graph of brightness over time, to view the data. For Kepler data, the bjd(date) column is the time in BJD. The dtr_flux stands for detrended flux, meaning that it should contain "cleaned" data.

First, I would plot the dtr_flux column over bjd(time) to obtain a lightcurve. Depending on the type of eclipsing binary, you should see a minimum and maximum dip occurring periodically. The data also contains a "phase" column, meaning the data has been "folded" to allow you to plot each cycle of the eclipsing binary on top of each other. See http://www.southampton.ac.uk/~sdc1g08/BinningFolding.html

After that, you can take the FFT if you wish. Remember that since this is an eclipsing binary with both maximum and minumum brightness dips, the FFT will have a spike both at P and P/2.