A natural input system is described for creating and editing complex structures in a typeset application. The natural input system receives a typeset representation of an object and converts the typeset format to generate a standard digital ink representation. The natural input system provides the generated ink representation to a natural input application where can be manipulated by the user with a rich set of correction and editing features provided by the natural input application. Once the end user is satisfied with the recognition result in the natural input application, the natural input system receives the recognition result based on the modified digital ink representation. The natural input system may convert the received recognition result to the typeset application format and provides the modified typeset representation to the typeset application for merging into the document the user is editing.