If you know the parameters of the circle that encompasses the area you'd like to remove (ie, the center coordinates and the radius), you could just calculate the distance of all points to the circle's center and then eliminate all dots whose distance is less than the radius. This would work if all of the dots are on the same plane as the circle's center which appears to be the case.
Here's an example where x and y are the coordinates of your dots. c is the (x,y) center of your circle and r is the radius.
% create data
x = rand(1000,1);
y = rand(1000,1);
c = [.5, .5]; %[x,y] center of circle
r = 0.2; %radius
% Calculate distance to circle center
d = sqrt((x - c(1)).^2 + (y - c(2)).^2);
% find dots on/in circle
inCircleIdx = d <= r;
% remove dots on/in circle
x(inCircleIdx) = [];
y(inCircleIdx) = [];
