I have obtained the following figure using a 120x120 matrix and the surf function.

Is there a simple way to make the lines between different colors look smoother?
First of all, surf may not be the best way to display 2D-image - if you don't actually need the height information, imagesc will work just fine. Even better, it won't show the differently colored lines between hexagons, since it's not going through the colormap at intersections.
However, regardless of your approach, a low-resolution bitmap will not be automatically transformed into a "arbitrary"-resolution vector graphics - and you may not want that, anyway, if you use the figure to allow you to inspect at which combination of (x,y) you obtained at a given value.
There are three approaches to make your image prettier - (1) segment the hexagons, and use patch to create a vector-graphics image. (2) upsample the image with imresample. (3) create a RGB image and smoothen each color separately to get softer transitions:
%# assume img is your image
nColors = length(unique(img));
%# transform the image to rgb
rgb = ind2rgb((img+fliplr(img)),jet(nColors)); %# there are much better colormaps than jet
%# filter each color
for i=1:3,rgbf(:,:,i)=imfilter(rgb(:,:,i),fspecial('gaussian',9,3),'replicate');end
surffunction, not by me. But I guess that the only option is to tune the image myself, or use another software to manage the data. - Beni Bogosel