Ion implantation systems are the mechanisms utilized to dope semiconductor substrates with dopants or impurities in integrated circuit manufacturing.  In such systems, a dopant material is ionized and an ion beam is generated there-from.  The ion beam is directed at the surface of a semiconductor wafer in order to implant the wafer with the dopant element.  The ions of the beam penetrate the surface of the wafer to form a region of desired conductivity, such as in the fabrication of transistor devices in the wafer.  A typical ion implanter includes an ion source for generating the ion beam, a beamline assembly including a mass analysis apparatus for directing and/or filtering (e.g., mass resolving) the ions within the beam using magnetic fields, and a target chamber containing one or more semiconductor wafers or workpieces to be implanted by the ion beam. 
Ion implanters are advantageous because they allow for precision with regard to both quantity and placement of dopant within the silicon.  In order to achieve a desired implantation for a given application, the dosage and energy of the implanted ions may be varied.  The ion dosage controls the concentration of implanted ions for a given semiconductor material.  Typically, high current implanters are used for high dose implants, while medium current implanters are used for lower dosage applications.  The ion energy is used to control junction depth in semiconductor devices, where the energy levels of the beam ions determine the degree to which ions are implanted or the depth of the implanted ions. 
One commercially available ion implantation system uses an ion source that includes a source chamber spaced from an implantation chamber where one or more workpieces are treated by ions from the source.  An exit opening in the source chamber allows ions to exit the source so they can be shaped, analyzed, and accelerated to form an ion beam.  The ion beam is directed along an evacuated beam path to the ion implantation chamber where the ion beam strikes one or more workpieces, typically generally circular wafers.  The energy of the ion beam is sufficient to cause ions that strike the wafers to penetrate those wafers in the implantation chamber.  Such selective implantation thus allows an integrated circuit to be fabricated. 
However, while much thought and consideration is usually given to the orientation (e.g., tilt and/or twist, etc.)  of the ion beam relative to the wafer, ion implantation systems generally orient the ion beam relative to the mechanical surface of a wafer, with little to no consideration given to variations between the wafer's internal lattice structure and its mechanical surface.  Additionally, wafers are purchased with a nominal lattice structure relative to their mechanical surfaces.  In particular, the wafers are designated with Miller Index data, such as 1,0,0, which is indicative of the relative orientation of the lattice structure to the cut surface of the wafer.  However, imprecisions associated with the wafer manufacturing process can cause the actual orientation of the lattice structure to differ from this nominal value by up to a degree (e.g., “1,1,0”±Δ, “, 1,1,1”±Δ). 
The actual orientation of the ion beam to the lattice structure of a wafer is important because it can affect channeling, and more particularly the repeatability of channeling, among other things.  For example, in some situations it may be desirable to “align” the ion beam with the lattice structure so that few ions encounter the structure and the ions are thereby implanted relatively deeply into the substrate.  Alternatively, it may be desirable to somewhat “mis-align” the ion beam with the lattice structure so that some of the ions encounter some of the lattice structure and are blocked, slowed down or reflected thereby.  In either instance, improper alignment can lead to undesired degrees of channeling (e.g., too little or too much).  Additionally, the deviations from the nominal lattice orientation and the dimensions of features formed upon the wafer can affect shadowing, and adversely impact the implantation process and resulting devices.