Go to Atlas-topbar-default and you can see the mendix logo placed in the image widget you can delete that widget and you can add the image widget and you add your own logo or in the topbar.
Delete the image widget in Atlas top bar.
The easiest way to do this is to go to “Mendix Studio” – “Theme Customizer” and upload a new logo.
Or edit file ...\theme\web\custom-variables.scss:
In the Atlas top bar there is an Static image has applied if its not required you can able to remove that.
Attached the screenshot for reference.