FSx Launch Batch Script

In addition to the Windows tasks scheduler suggestion:

• You could leverage this solution / blog to schedule a customized lambda that does the cleaning required if you can break up your cleaning steps (Lambda has a 15 minutes limit): https://aws.amazon.com/blogs/storage/enabling-smb-access-for-serverless-workloads/
• If you are running elaborate tasks, you could leverage a pre-configured ECS or Fargate image (fargate ain't supported after all): https://docs.aws.amazon.com/prescriptive-guidance/latest/patterns/run-event-driven-and-scheduled-workloads-at-scale-with-aws-fargate.html

One way to do this would be to use Windows Task Scheduler (presuming that you're running a Windows instance).