No there isn't a simple way to do that type of clipping with markers. In fact, you wouldn't believe how much work we do to get markers to do anchor point clipping.
If you really need this (and the 3d or gradient look), then your best bet would probably be to write a function that made markers out of "regular" geometry. Here's a really simple example:
function my_markers(x,y,w)
[sx,sy,sz] = sphere;
z = zeros(size(x));
npts = size(x,1);
for i=1:npts
surface(x(i)+sx*w/2,y(i)+sy*w/2,z(i)+sz*w/2, ...
'FaceColor',[.929 .694 .125],'EdgeColor','none', ...
'FaceLighting','gouraud')
end
I can use that function like this:
my_markers(randn(100,1),randn(100,1),.5)
xlim([-2 2])
ylim([-2 2])
axis equal
camlight
%
