Electronic ink layout analysis systems and methods provide flexibility and efficiency in organizing, analyzing, and processing digital ink. These layout analysis systems and methods allow users substantial freedom in entering electronic ink into a pen-based computer system. Using these systems and methods, a user's input digital ink is not constrained by requirements that a user write in a specific screen orientation, that a user write in one specific orientation on all portions of a page, or that a user write using a specific minimum or maximum sized stroke. Rather, the systems and methods freely allow the user to write anywhere on a given page, in any orientation or size, while still enabling effective and efficient handwriting recognition and other processing of the input digital ink.