The sensible answers have already been given. I'll just add the MIMT way of doing this.
instack = mimread('sources/birds*.jpg');
instack = imstacker(instack,'size',[500 500],'gravity','c','padding',0);
The result is a multiframe stack of all images, with each image centered and padded with black to fit a fixed geometry. You can use imfilter directly on this 4D array with whatever kernel you want:
filteredpict = imfilter(instack,fkgen('ring',20),'replicate');
Though like Image Analyst already pointed out, imfilter() already handles edge padding in a number of selectable ways, so manual padding isn't even necessary unless you need the images to share geometry for some other purpose.
Since you're reading PNG files (despite calling them jpegFiles), I'll note that unlike imread(), mimread() actually tries to preserve alpha content on import, and imstacker is greedy about array expansion, so you're likely to get an RGBA image when you're done. You can just strip off the fourth channel, or if you want to work with RGBA, you could set padding to [0 1] to specify that the padding has solid alpha. Imshow() doesn't know what to do with an RGBA or multiframe image, but imshow2() from MIMT does.
MIMT is a FEX thing:
This isn't exactly a serious suggestion, but I might as well throw it out there.