Our Rancher clusters were created not from RKE. I am storing my Rancher clusters etcd backups in S3 bucket. When I am trying to restore them, I am ending up in a problem. When I am using "rke up" and rke commands, it is popping up rke is not installed. When i tried to install rke in cluster CLI, there cluster.yaml file is not available. I can restore them ETCD backup's from rancher UI. But , I want to restore from backup's that are store in s3 bucket.

You should be able to run rke up on your local workstation using these options https://rancher.com/docs/rke/latest/en/etcd-snapshots/restoring-from-backup/#example-of-restoring-from-a-snapshot-in-s3