The PDF file’s source begins with %PDF. The application checks to see if the file is truly a PDF File. If it is not, it will return this error. Make sure that you list the PDF filename before the FDF filename on the command line. If the FDF filename is before the PDF file name, the application will return an error message.
fdfmerge sample.pdf sample.fdf
fdfmerge sample.fdf sample.pdf (Wrong!)