If you use your brower's Find (or Search) option to search this Forum's Post-page for the word 'stain', you'll find a number of posts that Henry and others have put up regarding stains on hardwood, drywall, and the like. Do search the ENTIRE post-page for this word because the first few do not directly address hardwood floors.
In any event, as Henry has stated, bleaching is definitely the first options. Replacing boards is the last. What I do want to add is that since you're going with the natural wood look, make sure the wood is sealed with a hardwood sealer. There are a number of sand sealers on the market. Normally, when a floor is stained, a sealer is contained therein to help prevent the problem you're having. Polyurthane is NOT a sealer. It is a protector from scratches, dents, and the like. If the wood isn't sealed and the polyurthane finish wears off, and coffee was spilt in that area, you'd have a deeper problem than you'd like.
My best to ya and hope this helps.
PS: Henry - I actually waited 'till you said somethin' on this one. (You're usually there for these!) ;-)