removing isapifilter problems

I am trying to remove a no longer used isapifilter with powershell.

Here is what I am doing,  this removes it from the server level but does not remove the one loaded at the web site level. 

Thank You anyone that can guide me.

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Import-Module WebAdministration

# remove millsecure if it is loaded

$isapiFilterName = 'millsecure'

$iispathFilter = 'iis:\'

cd iis:\

iisreset /stop

if (Get-WebConfigurationProperty -filter //isapifilters -pspath $iispathFilter -name Collection[name="$isapiFilterName"]) {

     Remove-WebConfigurationProperty -filter //isapifilters -pspath $iispathFilter -name Collection[name="$isapiFilterName"] }