@Filipe Souza (IT - Infra-SDT)
Thank you for posting this in Microsoft Q&A.
As I understand you have MDE extensions installed in your environment for VM's. However, CIS Microsoft Azure Foundations Benchmark v2.0.0 policy still show my VMs as non-compliant.
If the CIS Microsoft Azure Foundations Benchmark v2.0.0 policy is still showing your VMs as non-compliant, there might be some other issues
Check if the MDE extension is enabled and running on your virtual machines. You can do this by going to the Azure portal, selecting the virtual machine, and then checking the Extensions tab. Make sure that the MDE extension is listed, and its status is reported as "Running".
If it is enabled, then make sure that it is reporting data to Azure Security Center. You can check this by logging in to Azure Security Center.
If above mentioned is already confirmed than you can check and confirm if the CIS Microsoft Azure Foundations Benchmark v2.0.0 policy is properly assigned to your subscription or resource group. You can do this by going to the Azure Policy dashboard, selecting the policy, and then checking the Assignments tab.
You can check and confirm if all the virtual machines are properly tagged as CIS Microsoft Azure Foundations Benchmark v2.0.0 policy requires that all virtual machines are tagged with the "Owner" and "Environment" metadata
Let us know if you have any further questions on this.
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