Since you didn't specify it in the print command, MATLAB will print the current figure each time. In your case, since you have 6 figures, you need to tell MATLAB which one you want to print.
You could maintain a list of the 6 figures you create and then use that list in the call to print:
figs(1) = figure;
figs(2) = figure;
Or, if you always want to print all of the figures that you have created, you can ask MATLAB to give you the list:
figs = findobj(0, 'type', 'figure');
Then, print the figures. In the loop below I'm using sprintf() to "build" the output filename by * starting with a common basename: 'file', * adding the loop index, * and appending '.eps' to the end, so we get file1.eps, file2.eps etc:
print(figs(k), '-depsc', sprintf('file%d.eps', k))