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Go to Registered Domains on the left sidebar of the Route53 dashboard.
Click on your domain name.
In the top right corner, click on the Add or edit nameservers button under the Name servers section.
Click the x beside all of the default Route53 nameservers, removing them.
Add the two Nameservers that Cloudflare gives you, leaving the third box blank.
Click on the blue Update button. Click on Confirm if needed.