You can't create PDF with free Adobe Reader, you need to have Adobe Acrobat to do that.
If the software that came with your scanner can't save the scan as PDF you have to use Adobe Acrobat to do that.
With Adobe Reader you can only view, fill form fields, sign and add comments to a PDF. Take a look at Adobe Reader XI/Features and http://helpx.adobe.com/reader.html.
Adobe Acrobat allows you to create PDF from scanner: