Spiral bevel gears and hypoid gears can be machined using either face milling or face hobbing. A six-axis CNC bevel gear-cutting machine offers the flexibility required for various types of bevel gear manufacturing. Due to the complexity of the cutting motion, which involves multi-axis non-linear simultaneous movements, commercial software like VERICUT is used to simulate NC codes. This helps prevent tool path errors that could lead to machine collisions or inaccuracies during gear cutting. Simulation software often generates the simulated result of the machined gear as a triangular mesh (an STL output file), which can be further analyzed for flank error evaluation. This study presents a method for error analysis between the simulated and theoretical gears, allowing for verification of the accuracy of the NC program’s tool path. The process begins by inputting the gear parameters and loading the nominal data of the tooth surface and the gear’s STL file. The theoretical gear is transformed into the same coordinate system as the simulated gear through a series of coordinate transformations, and it is then rotated to align with the STL tooth surface, after which the tooth surface error is evaluated. This study analyzes a pair of hypoid gears manufactured using the face milling method as a numerical example. The results show that the deviation of the tooth surface is less than 0.07 mm, confirming the accuracy of the generated NC program.