The easiest way is to continue with the algorithm where you save the level-2-contours with a level one contour inside. Then you can reasonably easy remove all the level-2-contours, if you read the help and documentation to contour you will see that the second output is the handle (matlab type: matlab.graphics.chart.primitive.Contour) You can go in to the properties of that handle. But to me it seems easier to just delete that one and then plot the ones from the contour-coordinates you have saved:
[X,Y,Z] = peaks(1000);
figure(1),hold on
view(2);
colorbar('vert');
s = surf(X,Y,Z,'Facealpha',0.75,'Edgecolor','none');
% threshold = -0.3*max(Z,[],'all');
threshold1 = [-6, -6];
threshold2 = [-3, -3];
[c1,h1] = contour(X,Y,Z,[threshold1 threshold1],'-k','Linewidth',5);
[c2,h2] = contour(X,Y,Z,[threshold2 threshold2],'-k','Linewidth',5);
hold off
% Insert code to extract the contour-coordinates you want
[c2X,c2Y] = your_contour_selector(c2,c1);
delete(h2)
for i1 = 1:numel(c2X)
plot(c2X{i1},c2Y{i1},'k','linewidth',5);
end
HTH
