I might have misinterpreted your question ...
To plot a marker at a particular index of a list of (x,y) values, try this example
xy = rand(10,2) ;
IX = 3 ; % mark point 3
plot(xy(:,1),xy(:,2),'b-') ; % blue lines
hold on ;
plot(xy(IX,1),xy(IX,2),'rs') ; % red square marker
hold off ;
Note that you can combine the two plot commands into a single one.
