Accurate physical measurement of system geometric misalignments is difficult, so an accurate method of estimating the geometric parameters is needed. Several methods have been proposed that involve measuring projections of spheres at multiple projection views. For high resolution microCT systems, the estimation accuracy of the projected position of the sphere center is a critical factor in determining the geometric parameter accuracy. We have investigated several methods for improving the sphere center estimation. We simulated spheres of varying diameters and used several methods to estimate the positions of the projected sphere centers. The estimated center positions served as the input to methods for estimating the geometric parameters in order to assess the effect on geometric parameter accuracy. The center estimation methods investigated included computing the centroid and fitting the projection with a Gaussian or the analytic equation for the cone beam projection of a sphere. We found that the differences between the true and estimated projected center positions were smaller when fitted with the sphere's projection equation. In addition, using smaller spheres resulted in improved estimate accuracy. Using a phantom consisting of three 1 mm diameter spheres and with curve fitting to estimate the position of the spherical center, we were are able to obtain artifact-free reconstructions for a 42 μm pixel size on our prototype physical microCT system.