Traditional floorboards are fitted with 'brad' nails... http://www.bricksandbrass.co.uk/images/diy/floornails.jpg They are meant to be seen, finishing flush with the top surface of the floorboard. When people lift up carpets to expose their existing floorboards, they are usually not that visible, having blended in with the floorboards over time. It's only when people sand up and varnish their existing boards that they become more visible. However in your case of using reclaimed boards, it sounds like your builder is using nails that look far too new and shiny, rather than sourcing some that would've blended in better. One solution is to 'punch' the nail heads so they sit a few mm below the surface of the board. If they still stand out visually, the gap can be filled with a matching wood filler to hide the nail head completely. I hope you are taking notes reren ;-)