Place the document in the scanner and start Acrobat 9. Click the Create Task button and then select PDF From Scanner (or choose File > Create PDF > From Scanner).
Select Custom Scan.
Select your scanner from the Input options and any other appropriate settings (such as Color Mode and Resolution).
In the Output section, select Append to existing file or portfolio and browse for your target PDF Portfolio (or PDF file if you simply wish to add pages to an existing PDF file).

Click the Scan button and Acrobat will ask you for a file name (if you are appending a PDF Portfolio). The scanning process progresses and, when complete, the target portfolio will be opened automatically with the newly-scanned document included.
I was the guest presenter an AcrobatUsers.com eSeminar this past week. The topic was Scanning and OCR in Acrobat 9. This one-hour eSeminar is available for viewing online and covers this and other amazing scanning and OCR capabilities of Acrobat 9.
Learn how to make your PDF files interactive and capable! Sign up for my live, online Acrobat 9 Professional class.
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