A system comprising: a computing device; modeling software executing on the computing device, wherein the modeling software comprises: a rendering engine that renders a three-dimensional digital representation of at least a portion of a dental arch within a user-interactive computer environment; and a software module that provides a user interface to manipulate a digital representation of a temporary anchorage device relative to the digital representation of the dental arch to specify a virtual implant site for the temporary anchorage device, the computing device being configured to update a database associated with a patient record to record temporary anchorage device prescription data as specified by a practitioner, the temporary anchorage device prescription data including a selected temporary anchorage device (24; 138; 184) to be used, the temporary anchorage device implant site, and an orientation of the temporary anchorage device (24; 138; 184) within three-dimensional space before and/or after implantation, and/or a depth of implantation; and a manufacturing facility comprising: a prototyping instrument in communication with the computing device and configured to fabricate an orthodontic surgical guide (30; 130; 150; 180) in accordance with the specified virtual implant site, wherein a computing device of the manufacturing facility is configured to utilize the three-dimensional digital representation of the dental arch, comprising three-dimensional surface data related to an occlusal surface of the dental arch, and the temporary anchorage device prescription data to drive the prototyping instrument to form the surgical guide (30; 130; 150; 180) to have an alignment surface that matches a surface profile of the occlusal surface of all or a portion of the dental arch. a computing device; modeling software executing on the computing device, wherein the modeling software comprises: a rendering engine that renders a three-dimensional digital representation of at least a portion of a dental arch within a user-interactive computer environment; and a software module that provides a user interface to manipulate a digital representation of a temporary anchorage device relative to the digital representation of the dental arch to specify a virtual implant site for the temporary anchorage device, a rendering engine that renders a three-dimensional digital representation of at least a portion of a dental arch within a user-interactive computer environment; and a software module that provides a user interface to manipulate a digital representation of a temporary anchorage device relative to the digital representation of the dental arch to specify a virtual implant site for the temporary anchorage device, the computing device being configured to update a database associated with a patient record to record temporary anchorage device prescription data as specified by a practitioner, the temporary anchorage device prescription data including a selected temporary anchorage device (24; 138; 184) to be used, the temporary anchorage device implant site, and an orientation of the temporary anchorage device (24; 138; 184) within three-dimensional space before and/or after implantation, and/or a depth of implantation; and a manufacturing facility comprising: a prototyping instrument in communication with the computing device and configured to fabricate an orthodontic surgical guide (30; 130; 150; 180) in accordance with the specified virtual implant site, wherein a computing device of the manufacturing facility is configured to utilize the three-dimensional digital representation of the dental arch, comprising three-dimensional surface data related to an occlusal surface of the dental arch, and the temporary anchorage device prescription data to drive the prototyping instrument to form the surgical guide (30; 130; 150; 180) to have an alignment surface that matches a surface profile of the occlusal surface of all or a portion of the dental arch. a prototyping instrument in communication with the computing device and configured to fabricate an orthodontic surgical guide (30; 130; 150; 180) in accordance with the specified virtual implant site, wherein a computing device of the manufacturing facility is configured to utilize the three-dimensional digital representation of the dental arch, comprising three-dimensional surface data related to an occlusal surface of the dental arch, and the temporary anchorage device prescription data to drive the prototyping instrument to form the surgical guide (30; 130; 150; 180) to have an alignment surface that matches a surface profile of the occlusal surface of all or a portion of the dental arch.