It sounds like you have installed the software to use the scanner, but not the driver for the computer to recognize it. Right click on my computer, click properties, click the hardware tab and click device manager. If you see anything in that window that has a yellow question mark next to it, then you need to install the drivers, which are seperate to the user software.
If that is the case and you do need the driver, post your model and I will post a link to a download location.