So first plot:
clear all; close all;
figure; hold on
points=[0 0 0; 0.5 0 0; 0.5 0.5 0; 0 0.5 0; 0 0 0];
plot3(points(:,1), points(:,2), points(:,3),'c','linewidth', 2);
scatter3(points(:,1),points(:,2),points(:,3),40,'filled','k');

Yet no problems. Points plot with scatter3 show always on top of the line plots when I rotate the figure with the rotation tool.
Now!!
When I plot:
figure;
hold on;
points=[0 0 0; 0.5 0 0; 0.5 0.5 0; 0 0.5 0; 0 0 0; ...
0 0 1; 0.5 0 1; 0.5 0.5 1; 0 0.5 1; 0 0 1];
plot3(points(:,1), points(:,2), points(:,3),'c','linewidth', 2);
sc=scatter3(points(:,1),points(:,2),points(:,3),40,'filled','k');

And when I rotate the figure, the line plots are almost always on top of the scatter points (depending little bit from the angle), which is not what I want.
I have found some sort of solution which should work: uistack(sc)
It doesn't work though.
So what on earth should I do to make the scatter points show like in the first figure?? Thanks really much from the answer. This is really important for my master's thesis :D
