The loop scheme you have here is not serving any purpose. I suggest creating a function out of the lines of code that you have INSIDE the 5 for loops. Please refer the function page here.
Identify the inputs and outputs that you require for each set of data and use it to create the function. Call this function individually for each dataset. Do not number any of the figures inside the function. If all your plot (and/or subplot) data are available under your list of outputs for each set, it would also be best not to plot any figures inside the function at all. Once you have the results for all the datasets, you could simply pull up separate figures and do your plots in the end.
For example, say you are analyzing your third dataset. Let's say the inputs you pass are Response and Time, and the outputs you require are damping ratio ( Zeta), natural frequency ( Wn), damped frequency ( Wd) and transfer function ( h) The following is a big picture of what you would be doing:
[Zeta_3, Wn_3, Wd_3, h_3] = your_function_name(Response_3, Time_3)
Note the numbers attached to the input and output variables. These help you keep track of the dataset that you are currently working with. When defining the function, you do not need any such number referencing since you will be running all datasets through the same function. When plotting your graphs (outside the function), call up separate figure windows. For the third dataset above, the plot would be:
subplot(1,3,1), plot(Time_3, Response_3);
subplot(1,3,2), plot(Time_3, smooth(Response_3,20));
I have skipped the axes, titles and labels here but you could insert them as you normally would.