Hi,
if I am not mistaken, there are a couple of different ways to generate an eps export from matlab - and not all of them are good ways.
The preferred way would be to plot your surface as usual in matlab, then type "print -depsc <filename>" . I believe that this command accepts a sampling resolution as well (like -r600 or something like that).
The result should be a good input for converters to pdf.
You may also be interested in
http://www.mathworks.com/matlabcentral/ ... atlab2tikz which has a different way of integrating graphics from matlab into TeX: it reimplements the graphics using pgfplots. The font quality, consistency, size, and general appearance is typically better, albeit at a higher runtime cost and limited feature scope (pgfplots cannot do all that matlab can). Details in the link above and in the pgfplots manual (
http://pgfplots.sourceforge.net/)