You don't know. I don't know.
Your rogue knows. It's his job.
That's like asking "How does a wizard turn a little bit of bat guano into a big fireball? Nobody knows, but we don't have to know, because the wizard knows.
There are many things in this game that your character knows how to do but we players don't know how it's done. Disarming a spell/trap is one of those things.
But if you ask me, and I guess you did, I would say he 'erases' at least part of the spell, mainly by scraping off some parts of the magic rune(s) that were placed there when the trap was created (which is also an assumption; I don't think there is a rule that says spells used a trap must have written runes, but I assume they do). Those runes might be invisible to you and me, but he knows how to find them. It's his job. Then he scratches away at the outer edge, slowly removing more and more rune-stuff until eventually the spell/trap is disarmed. He might even know how to creep around in front of the rule without setting it off, maybe by covering himself in stuff that won't set off the trap or some such thing, so he can get in front of it to see it and scrape at it, all without triggering it.
