BoneJ can export STLs direct to file without displaying them
. But, I've noticed that the normals might have the wrong polarity (i.e. meshes are inside out). This seems to have been due to the mesher changing the order of Point3fs in the triangles / BoneJ using the wrong handedness of triangle, and so you might hit it depending on which version of 3D viewer you're using. In any case, MeshLab has a handy thing to invert normal directions.