This work presents an approach for the localization and control of helical robots during removal of superficial blood clots inside in vitro and ex vivo models. The position of the helical robot is estimated using an array of Hall-effect sensors and precalculated magnetic field map of two synchronized rotating dipole fields. The estimated position is used to implement closed-loop motion control of the helical robot using the rotating dipole fields. We validate the localization accuracy by visual feedback and feature tracking inside the in vitro model. The experimental results show that the magnetic localization of a helical robot with diameter of 1 mm can achieve a mean absolute position error of 2.35 ± 0.4 mm (n = 20). The simultaneous localization and motion control of the helical robot enables propulsion toward a blood clot and clearing at an average removal rate of 0.67 ± 0.47 mm3/min. This method is used to localize the helical robot inside a rabbit aorta (ex vivo model), and the localization accuracy is validated using ultrasound feedback with a mean absolute position error of 2.6 mm.