Refinishing wood floor
Painter's putty would work, but I don't know if it'd be your best option. 
First of all you'd need a ton of it to fill between every piece of flooring. Also, unless your going to use it after you put the finish on your floor, I'm not sure that the stain or lacquer wouldn't dissolve the putty. 
Unfortunately, I don't know what would be your best option, but I couldn't imagine that you should entertain the notion of painter's putty. I could be wrong, though...it certainly has happened before.....once...ha