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I have the front and back side scans of about 1000 separate documents in 2 sepatate folders. I'm looking to create a batch operation that combines the front scan and its corresponding back side scan into one document.

EDIT: I'm using Windows XP, The Scans are PDFs. The front covers are in one folder and the back covers are in another. The Files are named 1-1-NAME, 1-2-NAME; where NAME is a four letter idenifier.

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Please give some more informations: What OS are you using? What kind of documents (JPG, PDF)? Are the front covers in one folder and the back covers in the other? How are these files named? – mpy Apr 30 '13 at 14:41
Closely related: How to merge multiple PDF files onto one page with pdftk? – slhck Apr 30 '13 at 21:47

Are you looking for ImageMagick's montage? ImageMagick can work on pdf.

If you want something more flexible than ImageMagick montage, you can also write a simple script in Python language with pyPdf library. pyPdf can merge PDF pages and apply basic transformations (e.g. translation, rotation, scaling). Example script:

import pyPdf

def merge_horizontal(out_filename, left_filename, right_filename):
    """ Merge the first page of two PDFs side-to-side """

    # open the PDF files to be merged
    with open(left_filename) as left_file, open(right_filename) as right_file, open(out_filename, 'w') as output_file:
        left_pdf = pyPdf.PdfFileReader(left_file)
        right_pdf = pyPdf.PdfFileReader(right_file)
        output = pyPdf.PdfFileWriter()

        # get the first page from each pdf
        left_page = left_pdf.pages[0]
        right_page = right_pdf.pages[0]

        # start a new blank page with a size that can fit the merged pages side by side
        page = output.addBlankPage(
            width=left_page.mediaBox.getWidth() + right_page.mediaBox.getWidth(),
            height=max(left_page.mediaBox.getHeight(), right_page.mediaBox.getHeight()),

        # draw the pages on that new page
        page.mergeTranslatedPage(left_page, 0, 0)
        page.mergeTranslatedPage(right_page, left_page.mediaBox.getWidth(), 0)

        # write to file

def mkdir_p(path):
    except OSError as exc:
        if not (exc.errno == errno.EEXIST and os.path.isdir(path)): 
if __name__ == '__main__':
    import sys, os, errno
    output_folder_name = sys.argv[1]
    left_folder_name = sys.argv[2]
    right_folder_name = sys.argv[3]
    left_files = set(os.listdir(left_folder_name))
    right_files = set(os.listdir(right_folder_name))

    # for every files that are in both left_files and right_files
    for f in left_files.intersection(right_files):
        output_file_name = os.path.join(output_folder_name, f)
        left_file_name = os.path.join(left_folder_name, f)
        right_file_name = os.path.join(right_folder_name, f)
        print 'merging %s and %s into %s' % (left_file_name, right_file_name, output_file_name)
        merge_horizontal(output_file_name, left_file_name, right_file_name)

    # pair is missing, not merging
    print 'Only in left folder: ', left_files - right_files
    print 'Only in right folder: ', right_files - left_files

And call the script like the following:

python output_folder left_folder right_folder

Sample output:

merging folderA/two.pdf and folderB/two.pdf into output/dacd/adca/two.pdf
merging folderA/one.pdf and folderB/one.pdf into output/dacd/adca/one.pdf
merging folderA/three.pdf and folderB/three.pdf into output/dacd/adca/three.pdf
Only in left folder:  set(['four.pdf'])
Only in right folder:  set(['five.pdf'])
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