Background: Using cone-beam computed tomography (CBCT) in radiotherapy, the thorax or pelvis, which are both large areas, can be scanned by rotating the gantry 360° using a half-FAN (HF) bowtie filter (BF). The HF mode has a longer scan time than that of the full-FAN (FF) mode, thus exposing the patient to an increased imaging dose. Materials and Methods: To determine the applicability of FF to anatomically large areas, positioning error values and absorbed dose of organs at risk (OARs) were measured when HF and FF were employed in 22 patients who underwent pelvic intensity-modulated radiation therapy. Results: In a clinical experiment applying FFBF scan mode to anatomically large areas of a patient’s body during CBCT, the positioning error values were measured for all target areas within the mean ± 3 mm in all three directions. The scanning time in the FF scan mode was reduced by 20 s, while the absorption dose was reduced by 7–52 times in the OARs. Conclusion: The appropriate application of FF for treating large-size targets can reduce the CBCT scanning time, which, in turn, would markedly decrease the radiation exposure in patients by reducing random errors during procedures.