Could not find a solution to this using scatter or bubblechart. But for now I have a work around using the rectangle function based on another answer here. This works but it is not possible to make the circles transparent in this
%% Circles w same base and xy= left bottom corner
Xbottom=[1:6]';
Ybottom=[1:6]';
Couter= rand(6,1)*6;
Csize=[Couter/2 Couter/3 Couter/7];
Colmap=lines(3);
figure
arrayfun(@(x,y,diameter) rectangle('Position', [x, y, diameter, diameter], 'Curvature', [1 1], 'EdgeColor', 'k','FaceColor',Colmap(1,:)), Xbottom, Ybottom, Couter);
for ii=2:size(Csize,2)
arrayfun(@(x,y,diameter,diameter_outer) rectangle('Position', [x+diameter_outer/2-diameter/2, y, diameter, diameter], 'Curvature', [1 1],'EdgeColor', 'w','FaceColor',Colmap(ii,:)), Xbottom, Ybottom, Csize(:,ii),Couter);
end
axis equal