Zernike polynomials are an orthogonal set over a unit circle and are often used to represent surface distortions from FEA analyses. There are several reasons why these coefficients may lose their orthogonality in an FEA analysis. The effects, their importance, and techniques for identifying and improving orthogonality are discussed. Alternative representations are presented.© (2002) COPYRIGHT SPIE--The International Society for Optical Engineering. Downloading of the abstract is permitted for personal use only.