This paper presents new methods for the optimal selection of anatomical landmarks and optimal placement of fiducial markers in image-guided neurosurgery. These methods allow the surgeon to optimally plan fiducial marker locations on routine diagnostic images before preoperative imaging and to intraoperatively select the set of fiducial markers and anatomical landmarks that minimize the expected target registration error (TRE). The optimization relies on a novel empirical simulation-based TRE estimation method built on actual fiducial localization error (FLE) data. Our methods take the guesswork out of the registration process and can reduce localization error without additional imaging and hardware. Our clinical experiments on five patients who underwent brain surgery with a navigation system show that optimizing one marker location and the anatomical landmarks configuration reduced the TRE. The average TRE values using the usual fiducials setup and using the suggested method were 4.7 mm and 3.2 mm, respectively. We observed a maximum improvement of 4 mm. Reducing the target registration error has the potential to support safer and more accurate minimally invasive neurosurgical procedures.