If you would like to bulk remove users from an App you can do so via the API, unfortunately there currently is not a way to bulk remove users via the GUI. To get started with our API please see the links below:
Getting Started With the Okta API - https://developer.okta.com/docs/api/getting_started/api_test_client
Application User Operations: https://developer.okta.com/docs/api/resources/apps#application-user-operations
If you have any further questions, please feel free to open a support case with Okta Support.
Thank you, Ruchir Parikh Technical Support Engineer Okta Global Customer Care