When applied to the measurement of smooth surfaces, coherence scanning interferometry can be described by a three-dimensional linear filtering operation that is characterized either by the point-spread function in the space domain or equivalently by the transfer function (TF) in the spatial frequency domain. For an ideal, aberration-free instrument, these characteristics are defined uniquely by the numerical aperture of the objective lens and the bandwidth of the illumination source. In practice, however, physical imperfections such as those in lens aberrations, reference focus, and source alignment mean that the instrument performance is not ideal. Currently, these imperfections often go unnoticed as the instrument performance is typically only verified using rectilinear artifacts such as step heights and lateral grids. If an object of varying slope is measured, however, significant errors are often observed as the surface gradient increases. In this paper, a new method of calibration and adjustment using a silica micro-sphere as a calibration artifact is introduced. The silica microsphere was used to compute the point-spread and TF characteristics of the instrument, and the effect of these characteristics on instrument performance is discussed. Finally, a straightforward method to correct for phase and amplitude imperfections in the TF is described using a modified inverse filter.