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When you deploy application using the deploy tool a new CloudFormation template will be created, if you want to delete all of the newly deployed infrastructure all you need to do is to delete that cloud formation. You should be able to go to CloudFormation and find a stack with your project's name, by deleting it you will remove all of the deployed infrastructure including and additional nested stacks created.
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Additionally, the AWS Toolkit itself can delete Elastic Beanstalk environments, Lambda functions, and ECS clusters, as well as deleting entire CloudFormation stacks. To do this, find the resource in the AWS Explorer (if that's not visible, use View -> AWS Explorer from main menu), then right-click and choose "Terminate" or "Delete" as appropriate. As Dror said, for anything that was deployed using a CloudFormation stack (like a serverless app that creates Lambda and API Gateway), you should choose the CloudFormation stack and delete that.