How did you generate those graphs? You have a file of samples?
You can't do a Fourier Transform as such on an array of samples.
What you can do is called a Discrete Fourier Transform and you have some options about how to go about it.
You can take all your data at once and transform it. You can break it into pieces if you think the frequency content is time varying.
Looking at your signals they appear to be the sum of a few sine waves with a bit of noise so I'd transform the whole chunk at once.
Do you have any software available? I think even Excel will do a DFT for you these days. Mathematica, Matlab, Maple, etc. certainly will.
For completeness this is the formula for a DFT on an array of \(\displaystyle N\) samples, \(\displaystyle x_0,x_1,\dots, x_{N-1}\)
[MATH]X_n = \sum \limits_{k=0}^{N-1} x_k \exp\left(\dfrac{-i 2\pi }{N}n k\right),~n = 0,\dots, N-1[/MATH]
There are better ways to calculate it though.