You can use combinations of figure() and subplot() to create multiple figure windows and axes() according to your requirement. For example
figure;
subplot(2,1,1)
plot(rand(1,10))
subplot(2,1,2)
plot(rand(1,10))
figure;
subplot(3,1,1)
plot(rand(1,10))
subplot(3,1,2)
plot(rand(1,10))
subplot(3,1,3)
plot(rand(1,10))
figure;
subplot(2,2,1)
plot(rand(1,10))
subplot(2,2,2)
plot(rand(1,10))
subplot(2,2,3)
plot(rand(1,10))
subplot(2,2,4)
plot(rand(1,10))
