Hello Eva,
Not sure, what exactly do you need to perform after alignment?
If you need to optimize the camera positions, then the following function should be used:
optimizeCameras(fit_f=True, fit_cx=True, fit_cy=True, fit_b1=True, fit_b2=True, fit_k1=True, fit_k2=True, fit_k3=True, fit_k4=False, fit_p1=True, fit_p2=True, fit_p3=False, fit_p4=False)
You may also need to use chunk.resetRegion() function to reset the position and orientation of the bounding box, that may be off from the camera alignment after referencing the model and optimization.