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If you want to view certificates installed by System account in an Azure VM, directly remote to the VM cannot view the certificates as you are login in as a remote account. I just found an easy way to accomplish this purpose by using PsTools.
- Download PsTools from https://technet.microsoft.com/en-us/sysinternals/bb897553.aspx.
- Copy the bits to the VM.
- Run command "psexec -i -s mmc" to view the wanted certificates.
PsTools is also a convenient way to let you run your program as System account. Just run "psexec -i -s cmd.exe", and do anything as System account in the popup command line.