It is not possible to exclude specific folders from being scanned, but it is possible to run a custom scan.
To run a custom scan, open Webroot and select PC security from the menu on the left.
Under the "scan" tab, select the "cutom scan" link.
This will bring you to a screen where you can choose a quick, full, deep, or custom scan.
You can choose "custom" and it will only scan the files that you select.