Independently, I'd suggest the rectangle and inpolygon functions. However, to find the points inside the rectangle, I'd use patch instead of rectangle, since it gives you access to the x and y values of the shape.
x=4*rand(1,10)+1;
y=2*rand(1,10)+2;
% view data
scatter(x,y)
hold on
p = patch([2,4,4,2],[2 2 4 4],nan);
axis([1 6 1 5])
% find data points inside rectangle
in=inpolygon(x,y,p.Vertices(:,1),p.Vertices(:,2));
% replot data inside shape, this time filled in
scatter(x(in),y(in),'filled')
hold off
