The days of needing a big, clunky scanner in your office are over. The iPad can easily scan documents. In fact, the apps on this list are far better than an old-fashioned scanner. They can allow you to edit documents, fax documents, save documents to the cloud, and one of them will even read the document back to you.
The actual scanning of the document is accomplished using the back-facing camera on the iPad. Each of these apps will cut the document out from the rest of the picture, so you'll just get the page you are wanting to scan, not the pen sitting right next to the document. When taking the picture, the scanner app will show you the grid it will use to cut the document out of the picture. This grid is editable, so if it doesn't quite get the whole document, you can resize it.
When scanning the document, it is important to wait until the words on the page come into focus. The camera on the iPad will adjust automatically in order to make the text on the page readable. For the best scans, wait until you can easily read the words.