I think you might have issue with dimensions early on.
Have you tried to see what
size(strain_seg)
length(strain_seg)
actually output? I'm guessing the strain_seg has a size of [65536 1] and the blackman has a size of [1 64], which is why you have to add zeroes. I would suggest transposing one of them using the ' operator:
M = length(strain_seg);
w = blackman(M);
xw = C.*w';
X = fft(xw)
With regards to plotting the fft of the windowed strain segment you would need to know the time the segment spans. Lets say the segment you are examining was taken over 10 ms:
Ts = 10e-3;
dt = 1/Ts;
freq = dt:dt:(dt*length(xw)+dt);
figure
loglog(freq,abs(X));
xlabel('Frequency /[Hz]')
ylabel('Magnitude of FFT')