At first select rectangle region with Bitmap.getPixels
Then avaluate lines which bound your shape.
Change evry pixel in pixels[] which is outsidebounds and set it to 0 (or other value, it will be background of image)
And recreate you image from new dataset.
EDIT: try to use clipping technics http://www.zetcode.com/gfx/java2d/clipping/ or http://www.roseindia.net/java/example/java/swing/graphics2D/clip-area.shtml in example rectangle was used but thos methodics allows any region