You can use interp2 to evaluate the surface at the X & Y coordinates of your scatter data.
Consider the following example:
% Make up some sample data
[sx,sy,sz] = peaks(12);
px = randn(1,100);
py = randn(1,100);
pz = 5*randn(1,100);
% draw the surface and points
h1 = surf(sx,sy,sz);
hold on
h2 = scatter3(px,py,pz,'filled');
% Evaluate surface's function @ point's X & Y
spz = interp2(sx,sy,sz, px,py);
% Build mask of points which are above surface
mask = pz > spz;
% Delete old scatter
delete(h2)
% Replace with two scatters with different colors
h3 = scatter3(px(mask),py(mask),pz(mask),'filled');
h4 = scatter3(px(~mask),py(~mask),pz(~mask),'filled');
h3.MarkerFaceColor = 'red';
h4.MarkerFaceColor = 'blue';
But you should read this blog post to understand some of the subtleties of how surface does it's interpolation before you go too far down this path.
