If the plot is on it's own figure, you can get the figure handle first:
hFig1 = figure;
plot(1:9, 'b-');
% more code to do stuff on other figures;
% Now switch back to the first figure:
figure(hFig1);
If you're on the same figure, you can use the axes handle to switch focus to the axes you want:
axes(handles.axes1);
plot(1:9, 'b-');
% Switch focus to second plot on the same figure.
axes(handles.axes2);
plot(sin(0:0.1:2*pi), 'b-');
% Switch back to axes #1
axes(handles.axes1);
plot(2:25, 'r-');
