I think your loop was still working. You should really start with a small example when you have nested loops. I replaced the inner two loops with vectorized code and still it took 20 seconds to get the outermost loop to 5. See my edit and comments below.
You should re-think what you want to calculate and how you want to do it.
clc;
clear variables;%don't use clear all, there is no reason to
close all;
im1=imread('peppers.png');
im3=im2double(im1);
im3=mean(im3,3);%convert RGB to grayscale
[n,m]=size(im3);
c1=0;
h = waitbar(0,'Calculating XXX please wait......');
k=1;l=1;tic
for l=0:1:m-1
for k=0:1:n-1
if toc>20,break,end%if it takes too much time, exit the loop
[y,x]=meshgrid(0:1:m-1,0:1:n-1);
a=x+1;b=y+1;
aaa=exp(-1i*2*pi*(k*x/n + l*y/m));
c= im3.* exp(-1i*2*pi*(k*x/n + l*y/m));
c1=c1+sum(c(:));
aa=l+1;bb=k+1;
im(bb,aa)=c1;
c1=0;
end
waitbar(l / m);
end
ims = im*255;
close(h)
