While doing "figure(1), figure(2),..." will solve the problem in most cases, it will not solve them in all cases. Suppose you have a bunch of MATLAB figures on your desktop and how many you have open varies from time to time before you run your code. Using the answers provided, you will overwrite these figures, which you may not want. The easy workaround is to just use the command "figure" before you plot.
Example: you have five figures on your desktop from a previous script you ran and you use
figure(1);
plot(...)
figure(2);
plot(...)
You just plotted over the figures on your desktop. However the code
figure;
plot(...)
figure;
plot(...)
just created figures 6 and 7 with your desired plots and left your previous plots 1-5 alone.