Without actually seeing an image I can't be sure but I think you can to do this with the bwareaopen function. See http://www.mathworks.com/help/images/ref/bwareaopen.html

There's bwconncomp command for matlab that will give you the connected components with different indices. Keep the index that you want and discard the rest. A good idea here would be to plot each of the connected components in separate plots and finding out the one you want. Also, if you're already sure about the connected components characteristics (such as largest in size), you can extract it directly. Here's the link: http://www.mathworks.in/help/images/ref/bwconncomp.html