You can apply an object’s transform to the object’s geometry directly, and then reset the position, rotation, and scale like so:
object.updateMatrix();
object.geometry.applyMatrix( object.matrix );
object.position.set( 0, 0, 0 );
object.rotation.set( 0, 0, 0 );
object.scale.set( 1, 1, 1 );
object.updateMatrix();
three.js r.69