The BEST practice for ensuring the integrity of the recovered system after an intrusion is to restore the OS, patches, and application from a backup. This will ensure that the system is in a known good state, without any potential residual malicious code or changes from the intrusion. Restoring from a backup also enables the organization to revert to a previous configuration that has been tested and known to be secure. This step should be taken prior to conducting a thorough investigation and forensic analysis to determine the cause and extent of the intrusion.