A document prototyping system, program product, and methods are provided to create a systems engineering prototype document. The system can include a database having a plurality of systems engineering document templates stored therein. Each of the plurality of systems engineering document templates includes a plurality of document sections. The system can also include user interface in communication with the database to provide access to the database by a user, a document browser in communication with the database and the user interface to browse the plurality of systems engineering document templates through the user interface, a document section selector in communication with the user interface to select a subset of the plurality of document sections from the plurality of systems engineering document templates responsive to the user, and a document section merger responsive to the document section selector to merge the selected sections into a new systems engineering prototype document having the subset of the plurality of document sections to thereby define a new systems engineering prototype document format.