A system and method for calibrating and positioning a radiation therapy treatment table with a high degree of precision and accuracy. The system and method comprising a treatment table for use with a radiation therapy system with radiographic indexing markers embedded or inlaid in the patient treatment table. The radiographic indexing markers having a density different from density of the table material, or a radio-frequency or magnetic contrasting matter, something that the imaging system and detector of the radiation therapy system can detect, so that when scanned, with or without a patient or phantom on the table, the precise location of the patient treatment table in the x, y and z planes is known. The radiographic indexing markers may also have the ability to be visually seen by the technician, doctor, physicist or other health care provider conducting the procedure. This is important so that the table may be reconstructed, alone or with a phantom on it, by the radiation therapy system software, providing a very good indication of where the table top is prior to treatment.