Use bwareaopen() to extract just the small blobs. Then call regionprops to get their centroids. See my Image Segmentation Tutorial to see how to find centroids: http://www.mathworks.com/matlabcentral/fileexchange/?term=authorid%3A31862
I don't know how to compare fingerprint images, or list of minutiae centroids. The whole image may be rotated with respect to a reference. Also, some centroid may be present in the reference but not in the test image, and vice-versa. People have made careers out of fingerprint image analysis and I'm sure the code can get very very complex. I don't even know the general algorithms they use but you can find them here: http://www.visionbib.com/bibliography/contentspeople.html#Face%20Recognition,%20Detection,%20Tracking,%20Gesture%20Recognition,%20Fingerprints,%20Biometrics
And you might want to check out this: http://www.csse.uwa.edu.au/~pk/Research/MatlabFns/#fingerprints
