Traditional methods of dental mold making are well known, such as those described in Graber, Orthodontics: Principle and Practice, Second Edition, Saunders, Philadelphia, 1969, pp.  401 415.  Typically, these methods involve forming an impression of the patient's dentition using a suitable impression material, such as alginate or polyvinylsiloxane (PVS).  Impressions of the upper jaw typically include the teeth, the palate and gingival tissue surrounding the teeth on the facial and lingual surfaces.  Impressions of the lower jaw typically include the teeth and gingival tissue surrounding the teeth on the facial and lingual surfaces.  Plaster is then poured into the impression to form a relief of the dental features.  The relief is a permanent, three-dimensional mold of the dentition and oral tissues. 
Improved methods of mold making include rapid prototyping.  Rapid prototyping is a technology which has developed in the last decade.  Through the use of modern solid modeling CAD packages, combined with laser systems and new materials, solid parts may now be generated directly from a computer model.  Examples of this technology include stereolithography (SLA), laminate object manufacturing (LOM), and fused deposition modeling (FDM), to name a few. 
Stereolithography is a method that employs an ultraviolet laser to cure a thin layer of liquid plastic into a solid.  The process operates by taking a thin layer of the light-sensitive liquid plastic and passing the laser beam over the points where the part is solid.  Once a pass is completed, another layer of the liquid is added to the existing part, and the process repeats until the full part height is achieved.  SLA parts are extremely accurate, and tend to have excellent surface finishes.  A variety of SLA materials are available for different purposes, including waxes, plastics, and flexible elastomers. 
Laminate object manufacturing builds a part by taking individual sheets of paper that have a layer of glue on one side and building up successive sections of a part.  As each layer is laid down, a laser beam passes over the edges of the part, detailing the part and separating the part from the excess material.  In addition, the laser beam creates a grid throughout the excess material.  After the final sheet is laid down, the part may be separated from the excess material by removing cubes of the grid in a systematic fashion.  LOM parts are accurate, and very easy to sand and paint.  LOM parts also have different strengths in different directions due to the paper layers. 
Fused deposition modeling is a process that most closely resembles a miniature glue gun.  In fused deposition modeling, a heat softening and curing plastic is melted in a small nozzle which puts down a very fine bead wherever the solid part is supposed to be.  FDM parts have a rougher surface finish than an SLA part, but typically are stronger and more durable.  In all cases, parts created by rapid prototyping methods are generated relatively quickly and are accurate to a few thousandths of an inch. 
Producing a dental mold with rapid prototyping methods requires the use of a computerized model or digital data set representing the dental geometry and tooth configuration.  The model is used to guide the mold making process to produce a replica or relief of the computerized model.  The resulting relief is a three-dimensional mold of the dentition.  This method of making dental molds is particularly applicable to situations in which multiple molds are needed to be produced.  In this case, one computerized model may be used to make a number of molds in an automated fashion.  In addition, this method is applicable to situations in which a mold of a tooth arrangement which differs from the patient's current tooth arrangement is needed to be produced or molds of multiple tooth arrangements which differ from each other and the patient need to be produced.  In either case, the computerized model of the patient's teeth may be manipulated to portray each new tooth arrangement and a mold may be produced to reflect each successive arrangement.  This may be repeated any number of times to derive a number of molds with differing tooth arrangements.  Such techniques may speed production time and reduce costs by eliminating the need for repeated casting and artistic resetting of teeth in traditional mold manufacturing. 
Series of dental molds, such as those described above, may be used in the generation of elastic repositioning appliances for a new type of orthodontic treatment being developed by Align Technology, Inc., Santa Clara, Calif., assignee of the present application.  Such appliances are generated by thermoforming a thin sheet of elastic material over a mold of a desired tooth arrangement to form a shell.  The shell of the desired tooth arrangement generally conforms to a patient's teeth but is slightly out of alignment with the initial tooth configuration.  Placement of the elastic positioner over the teeth applies controlled forces in specific locations to gradually move the teeth into the desired configuration.  Repetition of this process with successive appliances comprising new configurations eventually moves the teeth through a series of intermediate configurations to a final desired configuration.  A full description of an exemplary elastic polymeric positioning appliance is described in U.S. Pat.  No.  5,975,893, and in published PCT application WO 98/58596 which designates the United States and which is assigned to the assignee of the present invention.  Both documents are incorporated by reference for all purposes. 
To carry out such orthodontic treatment, a series of computer models or digital data sets will be generated, stored and utilized to fabricate a series of representative dental molds.  Typically, only the digital information related to the tooth arrangement will be stored due to cost and space limitations.  However, to form a properly fitting elastic repositioning appliance or other dental appliance, it will at times be necessary to include in the mold a patient's oral soft tissue, such as a palate, facial gingival tissue and/or lingual gingiva tissue.  This may be the case when adding accessories to a basic elastic repositioning shell, such as palatal bars, lingual flanges, lingual pads, buccal shields, buccinator bows or wire shields, a full description of which is described in U.S. Provisional Patent Application No.  60/199,649 filed Apr. 25, 2000, and the full disclosure is hereby incorporated by reference for all purposes.  These accessories may contact or interact with portions of the soft tissue requiring a mold of such tissues to properly position the accessory in or on the appliance.  In addition, this may be the case when producing traditional orthodontic retainers and positioners.  Traditional appliances may be used as part of an orthodontic treatment plan utilizing elastic repositioning appliances, particularly in the final stages of treatment.  During such stages, for example, any residual intrusion of the teeth due to the presence of elastic appliances may be corrected with the use of a traditional retainer.  Such retainers typically comprise a polymeric replica of the palate or portions of the gingiva which support metal wires which wrap around the perimeter of the teeth. 
Existing fabrication systems are generally run manually by generating a report of cases and providing it into the fabrication software.  Such fabrication systems had several disadvantages.  First, each mold was not uniquely identifiable.  Second, the molds were created with problems of holes, free-floating island structures, and unstable peninsula structures.  Third, the molds were too tall and used more resin than required.  Fourth, the molds were not packed efficiently on a tray.  Fifth, laser marks were sometimes not sharp. 
Thus, a need exists to promptly process treated three-dimensional (“3D”) jaw and teeth data to create, in an automated manner, 3D mold data for manufacturing.  Also created would be a 3D cutting path for automated cutting of aligners and 3D placement data for automated laser marking of aligners.  These are to be achieved while minimizing resin used to build a mold, minimizing time to build a tray of molds, maximizing automation by reducing manual cutting of aligner, manual laser marking and errors. 
In view of the foregoing, it would be desirable to have methods and systems to provide an automated or semi-automated manufacturing or fabrication process for high volume and high scale customized items such as dental aligners.