The importance of SIMS analyses for “N-doped” impurity alloyed niobium and other surface-alloyed materials continues to increase. A major hurdle is the uncertainty of instrument calibration due to changes in sample height either from sample surface topography or from the sample holder itself. The CAMECA sample holder design allows for many types of samples to be analyzed. However, a drawback is that the holder faceplate can bend, contributing an uncertainty in the relative sensitivity factor (RSF) used to quantify the SIMS results. Here, we describe an improved sample holder having a reinforced faceplate, which prevents deflection and reduces uncertainty. Simulations show that the new design significantly reduces deflection from 10 μm to 5 nm. Sample measurements show a reduction of RSF uncertainty from this source from 4.1% to 0.95%. Grain orientation has long been suspected to affect RSF measurement as well. A bicrystal implant standard, consisting of randomly oriented and [001] grains, was successively rotated 15° between analyses. It was observed that 20% of the analyses performed on the randomly oriented grain exhibited anomalously high RSF values as well as slow sputter rates. These features were associated with the changing grain normal orientation with respect to the primary Cs+ beam. The grain orientation associated with the rise in RSF was simulated and determined to be the [101] crystallographic plane, thus indicating that ion channeling was responsible for the significantly increased RSF. Focused ion beam analysis confirmed slower sputter rates for the cardinal crystallographic orientations, indicating that ion channeling occurred for each.