Described herein is a surgical instrument guide for use with a robotic surgical system, for example, during spinal surgery. In certain embodiments, the guide is attached to or is part of an end effector of a robotic arm, and provides a rigid structure that allows for precise preparation of patient tissue (e.g., preparation of a pedicle) by drilling, tapping, or other manipulation, as well as precise placement of a screw in a drilled hole or affixation of a prosthetic or implant in a prepared patient situation.