There is growing interest in the use of the filtered basis functions (FBF) approach to track linear systems, especially nonminimum phase (NMP) plants, because of its distinct advantages compared to other tracking control methods in the literature. The FBF approach expresses the control input to the plant as a linear combination of basis functions with unknown coefficients. The basis functions are forward filtered through the plant dynamics, and the coefficients are selected such that tracking error is minimized. Similar to other feedforward control methods, the tracking accuracy of the FBF approach deteriorates in the presence of uncertainties. However, unlike other methods, the FBF approach presents flexibility in terms of the choice of the basis functions, which can be used to improve its accuracy. This paper analyzes the effect of the choice of the basis functions on the tracking accuracy of FBF, in the presence of uncertainties, using the Frobenius norm of the lifted system representation (LSR) of FBF's error dynamics. Based on the analysis, a methodology for optimal selection of basis functions to maximize robustness is proposed, together with an approach to avoid large control effort when it is applied to NMP systems. The basis functions resulting from this process are called robust basis functions. Applied experimentally to a desktop three-dimensional (3D) printer with uncertain NMP dynamics, up to 48% improvement in tracking accuracy is achieved using the proposed robust basis functions compared to B-splines, while utilizing much less control effort.