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Filter2d is definitely the wrong function.
Simply create an image the size of your spectrum of the same data type (CV_32F) and use the circle function to draw a binary circle.
Mat mask = Mat(rows, cols, CV_32F);
mask.setTo(0);
circle(mask, Point(rows/2, cols/2), 50, 1.0, -1); //50 is the radius, 1.0 is the color, -1 means filled.
Then multiply your amplitude by the mask. Remember to undo the fft quadrant shift before doing the inverse DFT.