There are couple of ways to do it
1. plot something do this code
plot([1:10]);
set(gcf, 'PaperPosition', [0 0 5 5]); %Position plot at left hand corner with width 5 and height 5.
set(gcf, 'PaperSize', [5 5]); %Set the paper to have width 5 and height 5.
saveas(gcf, 'test', 'pdf') %Save figure
2. if you have installed latex then pdfcrop is already installed with it so you can do like this.
saveas(gca,'test.pdf');
system('pdfcrop test.pdf test.pdf');
3. you make your own save function and follow 1 or 2 or may be some other procedure to do it.
