You can save the default position of each of your plots or subplots and then reset to those values after creating the color bar. However, if you reset to the default values, the color bar might get pushed outside of the figure frame, so consider using the axes function as shown below.
I hope this helps:
clear
figure(99),clf
ax(1) = axes('Position',[0.1300 0.60 0.65 0.35]) ; % or: ax(1) = subplot(2,1,1) ;
pos{1} = ax(1).Position ; % save default values
x = [-pi:0.1:pi] ;
y = cos(x) ;
plot(x,y)
ax(2) = axes('Position',[ax(1).Position(1) 0.11 ax(1).Position(3) ax(1).Position(4)]) ; % or: ax(2) = subplot(2,1,2) ;
pos{2} = ax(2).Position ; % save default values
membrane % function that plots the MATLAB logo
cb_handle = colorbar ;
% reset axes positions to default values after creating colorbar:
ax(2).Position = pos{2} ; % or: ax(2).Position = ax(1).Position
