Try this (I'm skipping the scatter portion for this example and assuming that you want the 'caps' that seal the ends to have the same color as the cylinder).
First replace your last 3 lines with this
r = 0.025;
[X,Y,Z] = cylinder(r);
hsurf = surf (X,Y,Z, 'EdgeColor', 'none', 'FaceAlpha', 0.2); % capture the handle of the surf object
Then, to add the 'caps' on the end of the cylinder:
patch(X(1,:),Y(1,:),Z(1,:), hsurf.CData(1,:), 'FaceAlpha', 0.2)
patch(X(1,:),Y(1,:),Z(2,:), hsurf.CData(1,:), 'FaceAlpha', 0.2)
Add the 'EdgeColor', 'none' option if you don't want the edges of the 'caps' to show.
