We describe the application of CT-MRI fusion software for 3D conformal radiotherapy in two patients with localized prostate cancer who had significantly altered pelvic anatomy due to prior surgery. Patient A had a hemipelvectomy for fibrosarcoma and Patient B had an abdominoperineal resection (APR) for rectal carcinoma. Using the Picker AcQSIM 3D treatment planning software equipped with CT-MRI fusion capabilities, we were able to construct 3D conformal treatment plans for the two patients. The CT-MRI fusion was invaluable in the 3D conformal treatment planning of these cases with distorted pelvic anatomy. It allowed for accurate identification of the clinical target volume (CTV) and was also able to better visualize normal structures so that the radiation beams could be placed to minimize toxicity to the normal tissues.