Your directory is structured like this?
If so, then it sounds like you’re opening the .atom directory when you go to open my_project. You can just open my_project and none of the other stuff will show up.
More detailed: the tree-view actually lets you manipulate files on your hard drive. If you delete a file or directory from the tree-view, it gets deleted from your machine. The way to load a specific file or directory without displaying a bunch of other stuff is to tell Atom to open that specific thing. It will get added as a “root” folder on the tree-view.