Control of an invasive medical instrument during a medical procedure is achieved using a system that includes magnetic field-based location facilities. Magnetic field sensors are placed in a medical instrument, e.g., a probe, and in an interface device to enable respective positions of the probe and the interface device to be ascertained by a location processor when the sensors are exposed to a magnetic field. The interface device is disposed such that an operator can control the medical instrument and the interface device concurrently. A display device, which can comprise a virtual reality display, is responsive to movements of the interface device as determined by the location processor to control the medical instrument, invoke various functions of the system, e.g., image manipulation, and otherwise facilitate the medical procedure via a graphical user interface.