Sentence: "Not sure though but it 'seems' that the Newspaper has taken off certain/some articles related to/with Madoff and Ponzi scheme from its website."

My question: Could the adjective 'certain' be used in the sentence above ? If yes, then what meaning would it make in that context ? Besides also tell (just a confirmation) is I'm right in using the preposition "to" before the word Madoff ?

Yes, and yes.
The preposition "to" is fine. (related to Ponzi schemes)

"Certain articles" is fine.
It's probably better than "some," because it implies that the "removed" articles were selected on some "certain," perhaps common basis.
Thanks Avangi Emotion: smile