Certain aspects relate to a medical system that includes a robotically controllable field generator and an instrument guide. The instrument guide may guide a percutaneously insertable instrument along an insertion axis. The instrument guide may also be positioned on an electromagnetic (EM) field generator, where the EM field generator can generate an EM field. A first robotic arm may be coupled to the EM field generator and it may move the EM field generator and the instrument guide. The system then determines: an EM target positioned within a patient, and a registration that maps positions within an EM coordinate frame associated with the EM field to positions within a robotic coordinate frame. The system may also determine, based on the registration, a position of the EM target within the robotic coordinate frame. Based on the position of the EM target within the robotic coordinate frame, move the first robotic arm may move to align the insertion axis of the instrument guide with the EM target.