Zernike circle polynomials are in widespread use in the commercial software of interferometer. However, they are not appropriate for noncircular pupils, such as annular, hexagonal, elliptical, and rectangular pupils. The traditional wavefront fitting or analysis in interferometric software are all for circular pupils, although working with the corresponding noncircular masks. For wavefront fitting with complex pupils, the necessity of applying orthogonal Zernike polynomials is demonstrated. Besides, the conventional method of removing misalignment error is illustrated to be adequate for the complex pupil.