It depends on how you have the scan configured... If you look in the agent configuration it will tell you what portins of the drive are being ignored.
The default configuration excludes:
$Cookies$\*
$InternetCache$\*
$LocalAppData$\*
$LocalAppData$\..\Temp\*
$LocalAppDataLow$\*
$RoamingAppData$\*
$Windows$\Prefetch\*
$Windows$\SoftwareDistribution\*
*\System Volume Information\*