This documents describes among other things a normalizing stage apparatus, tools and methods. One example includes a base that defines a trajectory. A first stage is moveably coupled to the base and the first stage moves along the trajectory. A second stage is moveably coupled to the first stage and moves an instrument coupled thereto with respect to the base and the first stage. Before movement of the instrument, the first and second stages are in first positions desired (e.g. predetermined) distances from a target area in the body. Another example includes the first stage and a guide tube stop coupled with the first stage. A guide tube is coupled with the guide tube stop and extends through a guide tube stop lumen. The guide tubes outer perimeter is dimensioned and configured to snugly couple with the surface defining the guide tube stop lumen.