Read about inpolygon. This should help you.
M = 100 ;
N = 100 ;
x = linspace(0,1,M) ;
y = linspace(0,1,N) ;
[X,Y] = meshgrid(x,y) ;
% semi circle
O = [0.5 0. ]; % origin of circle
R = 0.3 ; % RAdius of circle
th = linspace(0,2*pi) ;
xc = O(1)+R*cos(th) ;
yc = O(2)+R*sin(th) ;
% Get points lying inside circle
idx = inpolygon(X(:),Y(:),xc,yc) ;
% plot
figure
hold on
plot(X,Y,'.r') ;
plot(xc,yc,'b')
plot(X(idx),Y(idx),'.k')
