Trajectory guide, access port, and fiducial marker alignment

A trajectory guide for introducing an instrument into a human or animal subject is described. A guide stem can be removed in sections without disturbing the aligned instrument. An access port portion of the trajectory guide can be left in place, without disturbing trajectory alignment, and can allow overlying skin to be sutured closed. The access port can provide infusate delivery, such as using an injection port, catheter or the like. A fiducial marker arrangement can provide easy and accurate trajectory alignment, for use with the present trajectory guide, another trajectory guide, or without any trajectory guide.