What I would try first is to use principal components analysis ("PCA") to identify the two axes. Use pca() if you have the stats toolbox. Then you can fit lines with polyfit() going through the points along each PC. Use the points at the limits to determine where the lines start and stop. Sorry, no I don't have code that does this already - I'd have to develop it just as you would.
Another method you might also try is RANSAC.