suppose you calculate the positions of your joints $p_i, i=1\ldots6$ using your homogeneous matrices.
The best solution in my experience is to plot the initial configuration e.g. like this:
// calc p for time t=0
f=figure(1);
plot3([0, p_1(1)], [0, p_1(2)], [0, p_1(3)]);
hold on;
plot3([p_1(1), p_2(1)], [p_1(2), p_2(2)], [p_1(3), p_2(3)])
.... // for all links
the thing is now, if you want to have a smooth animation, it is a bad idea to call the plot command each time because it needs some time.
The better solution is to update the coordinates of your figure.
// in a for loop i=1:length of you time vector
// calc p for time t=i*deltaT
set(f.Children(x), 'XData', [p_1(1), p_2(1)], 'YData', [p_1(2), p_2(2)], 'ZData', [p_1(3), p_2(3)])
where you have to figure out the correct child of you figure handle f, you can just hop trough the structure of f to find the right children.