@Ranjithkumar Duraisamy, thanks for posting in Q&A. For managing servers through Microsoft Defender for Endpoint (MDE), you need to ensure you have the appropriate licenses. Since you mentioned MDE Plan 2 is active, you're covered for the advanced features. However, for Defender for Servers, you need either:
- Microsoft Defender for Servers Plan 1 or Plan 2 (part of Microsoft Defender for Cloud) 1.
- Microsoft Defender for Endpoint for Servers.
Additionally, ensure your servers meet the minimum requirements for onboarding to Defender for Endpoint, such as supported operating systems and necessary configurations
https://learn.microsoft.com/en-us/defender-endpoint/minimum-requirements
For windows server, this can't be enrolled into Intune. We can configure integration of Microsoft Defender for Endpoint with Intune and follow the link below to use Intune endpoint security policies to manage Microsoft Defender for Endpoint on windows servers that are not enrolled with Intune
https://learn.microsoft.com/en-us/mem/intune/protect/mde-security-integration
In addition, please ensure the windows servers met the above requirement and onboard the device to Microsoft Defender for Endpoint to see if it can occur on Intune and Microsoft Entra ID.
The synthetic registration process can vary, but typically it should complete within a few hours. If there are delays, you can check the following logs: Event Viewer: Look for logs under Applications and Services Logs > Microsoft > Windows > User Device Registration.to see if there's any finding.
Hope the above information can help.
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