Hi Cherie.
When you connect a Canon all in one, the printer driver software manages scanner and printer like different devices. The lack of ink does not influe on scanning on this printer.
About the mess inside the printer, surely a fault may affect scanning, but the problem you get " \'Scanner is not available while in use by another application or user.\'" is generally caused by software issues.
The problem happens when the driver software looses access to the device because device control is assigned to a different software, or because the printer driver gets denied access to printer (OS denying access).
This cannot be caused by low ink levels, and hardware fault casing this message will be very unusual.
Before starting , ensure that you did reset the whole system, by dsconnecting power cord from both printer and Mac, then allowing five minutes to drain power. If you have a notebook, also remove main battery.Connect everything back and test again.
The first step in troubleshooting is reinstalling the printer drivers. If that does not help, uninstall the printer, update Mac OS, and then reinstall the printer again.
If you have misplaced the disk, download and reinstall drivers from Canon website. See:
Download software- Canon.If drivers and Mac OS update followed by drivers setup do not work, then there is a different application that is holding control of the scanner. Check newly installed applications, or applications that you have only recently started. Go to Activity Monitor and click All Processes to see the whole list of running applications and check which one is active. If another process is working in background it may hold control of the scanner. Go to Preferences and click on your account. Click the Login Items button and check if any of the programs looks unusual or may use the scanner. Try also creating a new user account and logging in with the new user. Do a scan and check if the problem persists.
Most of the time the problem is fixed reinstalling the printer software or updating Mac OS, if not simply by disconnecting power and restarting devices.
Good luck.
Ginko.