I visualise my object by adding the actual meshes to it. When I save the scene, these objects are also saved although they are only used to show the result in the editor. Is there any way to tell the editor to not save the object?
No but you could make your script smart enough that they remove the dummies again when no longer needed.
You could even tag them specially for this purpose (potentially you could then intercept the saving to get rid of them or write your own saving code which does)