How many points define the cylinder? do you actually have points in the plane or is it just filled in visually by matlab? Is the cylinder defined by the rectangles corners?
http://www.mathworks.com/matlabcentral/answers/100687-how-do-i-extract-data-from-matlab-figures using the steps from here you can extract the XYZ data from the figure you can figure out where the plane intersects the cylinder and determine the points on the plane. here the points would be the same XY of the top and bottom of the cylinder with the Z coordinate at what looks to be 0.6.
