As for the .env file You can simply open those file on github and click the delete icon on the top right

after this scroll to the bottom and commit the changes

and for the node_module folder: open the folder and click on the 3 dots on the right to delete the directory

for future make sure you add a .gitignore file

Just create a .gitignore file in the root folder and add .env and just any file you want git to ignore when you push changes to your repository.

Also, you can login to github from your browser, go to your repo, open the file you want to delete and click the delete button.