It looks like you are on the right track with your looping on the file names.
It is a little confusing adding the data as an additional field to your existing file list structure S, but it isn't wrong.
I'm not sure what csvread(F,1) does, in the documentation they describe using either just one argument, or additional arguments for starting row and column. I don't know what it does with only two arguments.
After the loop completes, k will equal the number of files, so your lines, eta = S(k).data ... west = S(k).data will only compute values for the last file.
You could either use a loop to assign those or I think this would work
data = [vertcat(S(:).data)]
eta = data(:,1)/100
north = data(:,2)/100
west = data(:,3)/100