Here's how you can automate removing direct membership rules in an SCCM collection with PowerShell.

Download this script on the Technet Script Repository

<# 
.NOTES 
    Created on: 5/22/2014 10:56 AM 
    Created by: Adam Bertram 
    Filename:   Remove-CMDirectoryMembershipRule.ps1 
    Credits:    http://www.david-obrien.net/2013/02/24/remove-direct-membership-rules-configmgr/ 
.DESCRIPTION 
    This script removes all direct membership rules from a specified collection name    
.EXAMPLE 
    .\Remove-CMDirectMembershipRule.ps1 -SiteCode 'CON' -SiteServer 'SERVERNAME' -CollectionName 'NAMEHERE'     
.PARAMETER SiteCode 
     Your Configuration Manager site code 
.PARAMETER SiteServer 
    Your Configuration Manager site server name 
.PARAMETER CollectionName 
    The collection name you'd like to remove direct membership rules from 
#> 
[CmdletBinding()] 
param ( 
    [Parameter(Mandatory = $False, 
               ValueFromPipeline = $False, 
               ValueFromPipelineByPropertyName = $True)] 
    [string]$SiteCode = 'UHP', 
    [Parameter(Mandatory = $False, 
               ValueFromPipeline = $False, 
               ValueFromPipelineByPropertyName = $True)] 
    [string]$SiteServer = 'CONFIGMANAGER', 
    [Parameter(Mandatory = $True, 
               ValueFromPipeline = $True, 
               ValueFromPipelineByPropertyName = $True)] 
    [string]$CollectionName 
) 
 
begin { 
    try { 
        if ([Environment]::Is64BitProcess) { 
            # this script needs to run in a x86 shell, but we need to access the x64 reg-hive to get the AdminConsole install directory 
            throw 'This script must be run in a x86 shell.' 
        } 
        $ConfigMgrModule = "$($env:SMS_ADMIN_UI_PATH | Split-Path -Parent)\ConfigurationManager.psd1" 
        if (!(Test-Path $ConfigMgrModule)) { 
            throw 'Configuration Manager module not found in admin console path' 
        } 
        Import-Module $ConfigMgrModule 
         
        $BeforeLocation = (Get-Location).Path 
    } catch { 
        Write-Error $_.Exception.Message     
    } 
} 
 
process { 
    try { 
        Set-Location "$SiteCode`:" 
        $CommonWmiParams = @{ 
            'ComputerName' = $SiteServer 
            'Namespace' = "root\sms\site_$SiteCode" 
        } 
        #HACK: This should be 1 WQL query using JOIN but it's not immediately obvious why that doesn't work 
        #Get-WmiObject -ComputerName $SiteServer -Namespace "ROOT\sms\site_$SiteCode" -Query "SELECT DISTINCT * FROM SMS_CollectionMember_a AS collmem JOIN SMS_Collection AS coll ON coll.CollectionID = collmem.CollectionID" 
         
        $CollectionId = Get-WmiObject @CommonWmiParams -Query "SELECT CollectionID FROM SMS_Collection WHERE Name = '$CollectionName'" | select -ExpandProperty CollectionID 
        if (!$CollectionId) { 
            throw "No collection found with the name $CollectionName" 
        } 
                 
        ## Find the collection members 
        $CollectionMembers = Get-WmiObject @CommonWmiParams -Query "SELECT Name FROM SMS_CollectionMember_a WHERE CollectionID = '$CollectionId'" | Select -ExpandProperty Name 
         
        if (!$CollectionMembers) { 
            Write-Warning 'No collection members found in collection' 
        } else { 
            foreach ($member in $CollectionMembers) { 
                Remove-CMDeviceCollectionDirectMembershipRule -CollectionID $CollectionID -ResourceName $member -force 
            } 
        } 
    } catch { 
        Write-Error $_.Exception.Message 
    } 
} 
 
end { 
    Set-Location $BeforeLocation 
}

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