I would like to find the contours, manipulate them, and then plot them.
This plots contours
x = 0:0.1:1; y = 0:0.1:1;
[X,Y] = meshgrid(x,y);
Z = sin(X).*cos(Y);
[con_mat, h] = contour(x, y, Z);
To get the contour information without plotting, can use contourc.
con_mat = contourc(x, y, Z);
However, there appears to be no built-in way to plot this "contour matrix".