Context. Constructing the relevant magnetic field lines from active region modelling data is crucial to understanding the underlying instability mechanisms that trigger the corresponding eruptions. Aims. We present a magnetic flux rope (FR) extraction tool for solar coronal magnetic field modelling data that builds upon a recent methodology. The newly developed method is then compared against its previous iteration. Furthermore, we apply the scheme to magnetic field simulations of active regions AR12473 (similar to our previous study) and AR11176. We compare the method to its predecessor and study the 3D movement of the newly extracted FRs up to heights of 200 and 300 Mm, respectively. Methods.The extraction method is based on the twist parameter Tw and a variety of mathematical morphology (MM) algorithms, including the opening transform and the morphological gradient. We highlight the differences between the methods by investigating the circularity of the FRs in the plane we extract from. The simulations for the active regions are carried out with a time-dependent data-driven magnetofrictional model (TMFM). We investigate the FR trajectories by tracking their apex throughout the full simulation time span. Results. Comparing the newly developed method to the previous extraction scheme, we demonstrate that this upgrade provides the user with more tools and less a priori assumptions about the FR shape, which in turn leads to a more accurate set of field lines. Despite some differences, both the newly extracted FR of AR12473 and the FR derived with the old iteration of the method show a similar general appearance, confirming that the two methods indeed extract the same structure. The methods differ the most in their emergence and formation stages, where the newly extracted FR deviates significantly from a perfectly circular cross-section (which was the basic assumption of the initial method). The propagation analysis yields that the erupting FR from AR12473 indeed shows stronger dynamics than the AR11176 FR and a significant deflection during its ascent through the domain. The modelling results are also verified with observations: AR12473 is dynamic and eruptive, while AR11176 only features an eruption outside of our simulation time window. Conclusions. We implemented a FR extraction method, incorporating mathematical morphology algorithms for 3D solar magnetic field simulations of active region FRs. This scheme was applied to AR12473 and AR11176. We find that the clearly eruptive FR of AR12473 experiences significant deflection during its rise. The AR11176 FR appears more stable, though there is still a notable deflection. This confirms that at these low coronal heights, FRs undergo significant changes in the direction of their propagation even for less dynamic cases.