Designing a 2d low pas filter in fourier domain for an image
It's been said so many times before that multiplying the Fourier transform coefficients of an image with a mask of ones and zeros in the frequency domain in order to achieve a short-cut to the ideal brickwall filtering in the time-domain is not a recommended method; and almost never preferred due to unavoidable, and unforeseen, errors it would introduce.

That being said, there are algorithms in computer geometry that describe how to approximate a cirle (or ellipse) on a discrete grid like that of a computer monitor. 

The following is a circle algorithm that I remember having taken from wikipedia a decade ago. I have no idea on how it works, but just put it here for your sake.

% MIDPOINT CIRCLE ALGORITHM
Nx=256;          % image pixel size
Ny=256;
I=zeros(Ny,Nx);  % image onto which the circle will be drawn

x0 = 128;     % circle centers x-y
y0 = 128;
r = 50;       % circle radius

% ALGORITHM :
% -----------
f = 1-r;
ddfx = 1;
ddfy = -2*r;

x = 0;
y = r;

I(Ny-y0-r+1,x0) = 1;
I(Ny-y0+r+1,x0) = 1;
I(Ny-y0+1,x0+r) = 1;
I(Ny-y0+1,x0-r) = 1;

while x&lt;y

    if f &gt;= 0        
       y = y-1;
       ddfy = ddfy + 2;
       f = f + ddfy;
    end%if

    x = x + 1;

    ddfx = ddfx + 2;
    f = f + ddfx;

    I(Ny-y0-y+1,x0 + x) = 1;
    I(Ny-y0-y+1,x0 - x) = 1;
    I(Ny-y0+y+1,x0 + x) = 1;
    I(Ny-y0+y+1,x0 - x) = 1;
    I(Ny-y0-x+1,x0 + y) = 1;
    I(Ny-y0-x+1,x0 - y) = 1;
    I(Ny-y0+x+1,x0 + y) = 1;
    I(Ny-y0+x+1,x0 - y) = 1;

end%for

figure,imshow(I)


The output will be your mask :



I think you can modify it to work for ellipse and some fill in effects...