An implantable applicator (10) has at least one guide channel (12) for guiding a radioactive seed or source (66) to a target region. A plurality of imageable fiducials (40) are configured for attachment to the patient adjacent the target region. Electromagnetic sensors (18, 20, 22, 20′, 42) are mounted to the applicator and the imageable fiducials. An electromagnetic tracking system determines the relative position of the applicator mounted sensors (18, 20, 22, 20′) and the fiducial mounted sensors (42). A localizing processor (52) generates a map of the sensors which is combined (56) with a high resolution image (46). A comparing processor (70) monitors for changes in sensor positions, generates a movement correction transform (72) which transforms (74) the planning image into a transformed planning image (76). A brachytherapy treatment processor (60) generates a treatment plan (60a) from the planning image or the transformed planning image for controlling an auto-loader (64) which moves the radioactive source or seed (66) through the channels (12) of the applicator (10).