This sounds like a use for imagesc(). While surf()/pcolor() associate the data values with the vertices, image()/imagesc() associate the data with the face centers.
N = 5;
H = magic(5)
% a bar3 plot with bar colors matching z-height
hb = bar3(abs(H));
for k = 1:numel(hb)
c = permute(reshape(hb(k).ZData,6,5,4),[1 3 2]);
c = permute(repmat(max(c,[],[1 2]),[6 4 1]),[1 3 2]);
hb(k).CData(:) = reshape(c,[],4);
end
% using imagesc() instead
figure
imagesc(H)
Of course, if you want the gaps between the faces, that might be a different story.
