I'm sure there are more qualified experts here but I've done my fair share of body work through the years starting with a 15 yr rusty Dodge Dart I inherited from my father when I was 17 (many many moons ago)...and ending with a 99 Jeep Wrangler I presently own.
And with that limited experience and from the pictures you've posted it appears you have more than just surface rust issues (which I believe what the OP of this thread had). Again, I'm only going from the pictures and can't tell what the actual size of the rusted area is but it looks as though you have a bit more extensive body work to do than what this thread was discussing.
If this were my floor, and if I believe the area is a large as I believe from the pictures you posted, I would be doing some major body work to stop any further corrosion than merely sanding and applying a corrosion-resistant barrier product. That would start with removing completely any metal around the hole (which would make those little holes one large hole) that have even a tiny bit of rust and then welding a new metal sheet around the open area. If the holes are indeed smaller than it looks from the pictures, you may get away with some other type of reinforcement that can merely be applied. Fortunately, because it is the floor and will be covered and not on the body where the weld will be seen, it wouldn't take a lot more body work afterwards to make it look good (ie, spackling, grinding, smoothing).
Again....I did not do this professionally but holes to me are always a different animal to attack than merely surface rust.