Do you have Adobe Acrobat? You cannot do this with the free Reader.
In Acrobat you can select to clean up your document either at scan time, or if you have a scanned document already saved as a PDF, at a later time. To clean up such an already scanned document, you would select Tools>Document Processing>Optimize Scanned Document.
This gives you a number of filters that will "optimize" your document:
When you click on the Edit button in the "Filters" section, you get the filters dialog, which allows you to straighten ("Deskew") the image, and do a few other things.
Unfortunately, this will very likely not get rid of your hole punch and staple artifacts. For this you either need to cover up or redact these areas, or use an external image editor for further cleanup. I use Photoshop for this, but it requires that you open it for every scanned page. You would select Tools>Content Editing>Edit Text & Images, then right-click on an image and select to edit it in Photoshop. Once you've cleaned up your image, you can then save the image in Photoshop and it will get imported automatically into Acrobat.
As I mentioned, another option is to cover up these areas with "whiteout" - you can use the drawing markup tools under the "Comment" header on the right side to do that. Just make sure that you select white as the border and the fill color. This will not permanently modify your document, you would still be able to recover your original content (even after flattening such a document). You can however use the redaction feature in Acrobat Pro to remove these elements in your scanned image completely. See this tutorial for more information: http://blogs.adobe.com/acrolaw/2007/12/cleaning_up_scanned_images/
Karl Heinz Kremer
PDF Acrobatics Without a Net
PDF Software Development, Training and More...
http://www.khkonsulting.com