How do I get transform.localScale (C#) to apply to a clone generated by an object rather than the object the script is attached to?

Welcome to Unity Answers!

If you know which GameObject you're interested in, you can set its local scale easily enough.

You didn't mention a language, so I'll assume JavaScript:

 var go : GameObject = ...     //some GameObject
 go.transform.localScale = ... //whatever you want

The hard part, then, is figuring out which GameObject you want to edit. Your scene could contain hundreds!

The best time to get a reference to a clone is right as its made. I assume you're using Instantiate to create the clone? It returns a reference to the cloned object. You can cache that reference:

 //assumes you're cloning a GameObject
 var clone : GameObject = Instantiate(...) as GameObject;
 clone.transform.localScale = ...

Depending on what exactly you're trying to do, you can edit the clone immediately, or you can keep track of it for a while and edit it later. In some cases, it might be useful to keep a collection of clones for later reference.