You're attempting to set up SharePoint scans without using the SharePoint Solution connector, following the Online Help Enabling SharePoint scanning without installing the SharePoint solution powershell script to enumerate the SharePoint sites to be scanned, and you get the error: "The term 'Get-SPWebApplication' is not recognized as the name of a cmdlet, function, script file, or operable program. Check the spelling of the name, or if a path was included, verify that the path is correct and try again."
The PowerShell module is not being imported into the PowerShell console.
You can add the module by running: 'Add-PSsnapin Microsoft.SharePoint.Powershell'
After adding the snapin, you can run the powershell script without getting the cited error.