Thanks for the post. If you are using the local edition of ClinicOffice (Startup, Professional, Server edition) then you can scan a new document by clicking on the "Acquire from" button, within the patient's document section and select your scanner from there.
If you are using the Hosted edition of ClinicOffice then, unfortunately, this feature is not available. The reason is that most scanners use either a TWAIN or a WIA driver, neither one of these two is Microsoft Remote Desktop compatible. This means that Hosted server cannot see the scanning and hence ClinicOffice is unable to see the scanner. You can still scan the document, save it locally and use the "Add Files" option instead, but you just cannot scan directly into the ClinicOffice Hosted edition because of this.