Intensity-modulated radiation therapy (IMRT) is one of the most complex applications of radiotherapy that requires patient-specific quality assurance (QA). Here, we describe a novel method of 3-dimensional (3D) dose-verification using 12 acrylic slabs in a 3D phantom (30 x 30 x 12 cm(3)) with extended dose rate (EDR2) films, which is both faster than conventionally used methods, and clinically useful. With custom-written software modules written in Microsoft Excel Visual Basic Application, the measured and planned dose distributions for the axial, coronal, and sagittal planes were superimposed by matching their origins, and the point doses were compared at all matched positions. Then, an optimization algorithm was used to correct the detected setup errors. The results show that this optimization method significantly reduces the average maximum dose difference by 7.73% and the number of points showing dose differences of more than 5% by 8.82% relative to the dose differences without an optimization. Our results indicate that the dose difference was significantly decreased with optimization and this optimization method is statistically reliable and effective. The results of 3D optimization are discussed in terms of various patient-specific QA data obtained from statistical analyses.