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Actually it does work. Twiddle the tolerances to get the results you would like. FeatureSets and python lists are interchangeable, so you can use list comprehension to filter them.

SimpleCV:30> squares = Image('./squares.png')
SimpleCV:31> blobs = squares.findBlobs()
SimpleCV:32> blobs.draw(width=-1)
SimpleCV:33> test = [b for b in blobs if b.isSquare(0.1,0.1)]
SimpleCV:34> test = FeatureSet([b for b in blobs if b.isSquare(0.1,0.1)])
SimpleCV:36> test.draw(color=Color.RED,width=-1)
SimpleCV:37> squares.show()
SimpleCV:37: <SimpleCV.Display Object resolution:((640, 480)), Image Resolution: (640, 480) at memory location: (0x107048710)>
SimpleCV:38> squares.applyLayers().save('squaresout.png')

Here are the results