I am trying to create a meshgrid without some of the points that falls within the circle having specified coordinates and a radius. I am not able to subtract the grid points
One can not simply remove points from a meshgrid. Instead, you should create another array Z as
Z
Z = numpy.where((X-circle_x)**2+(Y-circle_y)**2>r**2,1,0)
and plot it as
plt.scatter(X,Y,Z)