Removing a trusted Certificate Authority from “Trusted Root Certification Authorities” certificate store in Active Directory

Problem
You have previously deployed multiple Active Directory Enterprise Root Certificate Authorities in the domain and because you’ve had to redeploy the CA a few times using the same name, you notice that your domain joined workstations and servers now have multiple root certificates stored in the Trusted Root Certification Authorities certificate store:


Solution
I was unsure as to whether there was an easy way to remove these root certificates in the Trusted Root Certification Authorities certificate store so I went ahead and reached out to our Microsoft partner support and the response I received was to review the following KB article:
How to remove a trusted Certificate Authority from computers in the domainhttp://support.microsoft.com/kb/555894
The article’s instructions appear to be pretty straight forward as it demonstrates the user of a batch file and script to automate the process:


The first step was to download the following SDK:
Download:  Platform SDK Redistributable: CAPICOMhttp://www.microsoft.com/en-us/download/details.aspx?id=25281
The problem I immediately noticed was that there were a few typos in the script (namely the removeca.vbs filename):




… and when I finally launched it on a Windows 7 64-bit desktop, it would error out with:

C:\Temp\RemoveCA>c:\windows\system32\regsvr32 capicom.dll /s
C:\Temp\RemoveCA>cscript remove.vbs
Microsoft (R) Windows Script Host Version 5.8
Copyright (C) Microsoft Corporation. All rights reserved.
C:\Temp\RemoveCA\remove.vbs(13, 1) Microsoft VBScript runtime error: ActiveX com
ponent can't create object: 'CAPICOM.Store'
C:\Temp\RemoveCA>


Since it looks like Microsoft suggests to use logon scripts to clean up these root certificates, I simply went ahead and looked into using the certutil.exe command to remove certificates and then created a simplified batch file to remove the entries.
The first step was to determine the right syntax and it took quite a bit of time because I did not find the following TechNet article too straight forward:
http://technet.microsoft.com/en-us/library/cc732443(v=ws.10).aspx
In any case, the proper syntax is the following:
certutil -delstore -enterprise root "<Serial number>”
The command above will remove the certificate located in the Trusted Root Certification Authorities Computer Store of the workstation you execute this command.  To determine the serial number, simply open up the certificate’s properties and navigate to the Details tab, then select the Serial number field as such:


Copy the serial number and slot it into the end of the command added quotes:
certutil -delstore -enterprise root “5f 92 5c 79 5a 90 49 bc 4e e7 f7 96 fb c7 de 62”


Once the command successfully executes (it doesn’t take long), you will see the following output:
C:\>certutil -delstore -enterprise root "5f 92 5c 79 5a 90 49 bc 4e e7 f7 96 fb c7 de 62"
root
Deleting Certificate 5
CertUtil: -delstore command completed successfully.
C:\>
Proceed with testing this on a workstation with all of the certificates you intend on deleting one after another and copying and pasting the command into notepad as such:
certutil -delstore -enterprise root "55 8c 2e b5 cc ae 92 89 41 5b 25 33 f7 ef 6c 2e"
certutil -delstore -enterprise root "79 7a f4 a9 9e 81 79 ba 44 b5 91 bc 85 d0 b0 df"
certutil -delstore -enterprise root "58 35 46 65 2a 6e 47 93 48 31 62 3a 49 83 eb 24"
certutil -delstore -enterprise root "27 77 84 a8 49 39 3c b2 4e c7 e9 47 8f 1b 52 60"
certutil -delstore -enterprise root "58 ed e0 1e 68 68 06 a2 4b d3 14 5d 11 f2 7a 85"
certutil -delstore -enterprise root "2e cc 73 20 fe 05 0a 88 44 d8 fb 3a 96 1a 99 5a"
certutil -delstore -enterprise root "25 a5 76 4c c6 fb ca 8a 4d c1 bd 46 e4 9c 3c 37"
certutil -delstore -enterprise root "60 15 e8 95 34 09 ff a3 42 16 26 9a fc fd 67 29"
certutil -delstore -enterprise root "5f 92 5c 79 5a 90 49 bc 4e e7 f7 96 fb c7 de 62"


Once you have removed all of the certificates, save the notepad file as a batch file then take it to another workstation to execute verifying that all of the certificates you intend on deleting are removed.  Once you have validated that the batch file works as intended, proceed with creating a new GPO in your Active Directory and apply it to the OU with the workstations you want the certificates removed:


Note that I applied this batch file to the following policy setting:

Computer Configuration –> Policies –> Windows Settings –> Scripts –> Startup

Hope this helps anyone looking for a way to clean up their root certificates.