Not sure if this is what you are doing or not, but this seems to work for me. It works very nicely on lines (at least in my limited testing)
% find all objects with the property BrushData
hB = findobj(gcf,'-property','BrushData');
% extract the brush data
data = get(hB,'BrushData');
% find objects where BrushData is not all zeros (i.e. you have some points "brushed"). Note: this probably could be written in a cleaner fashion, but it shows you the idea. Then, index back into your list of objects and get the ones that were "brushed"
brushObj = hB(find(cellfun(@(x) sum(x),data)))