An inverse planning method that is capable of controlling the appearance of the implanted fiducial(s) in segmented IMRT fields for cine MV or combined MV/kV image-guided IMRT is provided. The method for radiation treatment includes computing a radiation treatment plan and delivering beams to a target in accordance with the radiation treatment plan, where computing the radiation treatment plan includes introducing a penalty in an inverse planning objective function optimization calculation to discourage or avoid blockage of one or more fiducials in optimized multi-leaf collimator (MLC) apertures.