The sample mounting system comprises a sample holder and a sample stage having a platform for supporting the sample holder. The sample can be fixed to the sample holder by a mount. The sample holder comprises a holder reference portion, which co-operates with a corresponding reference portion of the sample stage (the stage reference portion) to align the sample holder with the sample stage. When the sample holder is positioned on the platform such that the stage reference portion and the holder reference portion engage each other, the sample holder is aligned with the sample stage.