found the answer
figure1 = figure; figure2 = figure;
while i < 4
kS = kS_array(i);
bS = bS_array(i);
sim('sim_1');
set(0, 'currentfigure', figure1);
subplot(3,1,i), plot(time,x);
set(0, 'currentfigure', figure2);
subplot(3,1,i), plot(time, FT);
i=i+1;
end
This works the way I want it.