The invention is methods and systems for encoding geographic coordinates and features in a portable document format file. Various embodiments of the invention permit encoding of a geographic relationship between the coordinate system of a digital source map, and the rendering of that map to a portable document format (PDF) document as well as the information required to transform between the source map coordinate system and the PDF coordinate system. This encoding can be performed by determining the coordinates of the points of a polygon of selected source map data to be rendered to PDF in both PDF coordinates and source coordinates, and by determining a transformation matrix to convert the coordinates from one system to the other, including information regarding the geometric projection of the source coordinate system. Having encoded this data, it can be possible to obtain any location within the rendered PDF file in coordinates of the source coordinate system.