Después de buscar un rato encontré una solución que permite rápidamente convertir arvhivos pdf a texto plano. Incluso manteniendo el layout del archivo original. Se trata de Poppler.
pdftotext version 0.10.1
Copyright 2005-2008 The Poppler Developers - http://poppler.freedesktop.org
Copyright 1996-2004 Glyph & Cog, LLC
Usage: pdftotext [options] []
-f : first page to convert
-l : last page to convert
-layout : maintain original physical layout
-raw : keep strings in content stream order
-htmlmeta : generate a simple HTML file, including the meta information
-enc : output text encoding name
-listenc : list available encodings
-eol : output end-of-line convention (unix, dos, or mac)
-nopgbrk : don't insert page breaks between pages
-opw : owner password (for encrypted files)
-upw : user password (for encrypted files)
-q : don't print any messages or errors
-v : print copyright and version info
-h : print usage information
-help : print usage information
--help : print usage information
-? : print usage information