You can use bwareaopen() to get rid of blobs less than a certain size. If you have a bunch of other criteria, like circularity or solidity or whatever, then you can get rid of blobs by passing the list of indexes into ismember(). See my Image Segmentation Tutorial at http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862
binaryImage = bwareaopen(binaryImage, 8); % Only 8 pixels or bigger survive.
or
labeledImage = bwlabel(binaryImage);
indexesToKeep = [2,4,13,33]; % Whatever....
newBinaryImage = ismember(labeledImage, indexesToKeep) > 0;
By the way, in image processing we don't call them "clusters". They're called "blobs" or "connected components".
