It's likely you're confusing this with the fictional Baxter Building, which is Marvel's headquarters and is located in New York City. The Baxter Building has been destroyed on numerous occasions in Marvel Comics, often as a result of battles or attacks.
This is a sensitive topic due to the real-world tragedy of the 9/11 attacks. It's understandable to confuse fictional events with real ones, but it's important to be accurate in our understanding of events.