It depends on the type of scanner API your scanner and its software support. Please see:
https://en.wikipedia.org/wiki/Image_scanner#Applications_Programming_Interface[
^].
Depending on what is that, you can find appropriate implementation. In general case, it could be something like
http://bfy.tw/brl[
^].
To work with PDF, you can use iText, or its .NET port, iTextSharp:
http://en.wikipedia.org/wiki/IText[
^],
http://itextpdf.com/[
^],
http://sourceforge.net/projects/itextsharp/[
^].
In included the reference to Java iText site as well, because most documentation is there. If you understand C#, it would not be difficult to understand Java-bases API documentation.
—SA