Since you created the bounding boxes of the objects in the binary image, presumably with regionprops(), you already know their height and width of all the bounding boxes. You can keep certain ones by making a logical vector saying whether or not to keep it, then use that to extract only the ones you want to keep. For example if you only want widths > 30, you can do
props = regionprops(binaryImage, 'BoundingBox');
allBB = [props.BoundingBox];
allWidths = allBB(3:4:end);
keeperIndexes = allWidths > 30;
keeperProps = props(keeperIndexes);
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