A system and method for identifying and separating handwritten text from machine printed text in a document having a combination of handwritten text and machine printed text. In one embodiment, the present invention is installed as an intelligent printing control interface in a conventional computer and allows any document generated by any application to be selectively processed to remove any handwritten text prior to printing of the document, under the control of the user. In an alternative embodiment, the present invention is installed as an intelligent printing control interface in a conventional digital copy machine, which allows any document being copied to be selectively processed to remove any handwritten text prior to printing of the document, under the control of the user. The present invention employs a handwriting separation method which uses Hidden Markov Models to identify regions as either handwritten text or machine printed text.