Set the current figure with figure(hFig1) like nl2605 told you. But you say it's still not working like you'd want. The reason is . . . you can't do subplot(1, 2, 2) and then subplot(2, 1, 2) because the layout in the second case would "overlap" the layout in the first case, causing your first plots to vanish, which is what you're seeing. In the second case you have 2 plots taking up the left and right halves of the GUI. In the second case you have 2 rows (the same) but only 1 column. So plotting, say, the bottom half with (2,1,2) will cause that plot to "overlap" the bottom half of both images that you plotted before (in the left and right half), so the first two vanish. You need to decide where to put your plots so they don't overlap if you want them all to remain.