A method of operating a multi-axis machine. The machine linkage is monitored to detect an approach by linkage joint(s) toward singularity. A degree of the approached singularity is determined. The joint(s) approaching singularity are identified. Virtual joints are used to replace the identified joint(s) in a manipulator matrix to modify the manipulator matrix. The modified matrix is used to determine position changes for the linkage links. This method can provide software-based compensation for a wide range of machine configurations, without a priori knowledge of singularities for a given machine.