About to sand floor: should I worry about these black nail marks

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Hi,

I'm just about to undertake filling the gaps between our pine floorboards with slivers and so will end up having to sand the whole floor.

I am pretty confident in what I need to do, the only thing I am worried about is that most of the nail holes have black marks surrounding them. I assume these will all sand off and I was going to fill the holes with wood filler.

However, I am a bit worried that after all my work these black marks will return (they are obviously a result of something to do with the wood coming into contact with the nail).

Does anyone have any idea if they will?
 

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Looking at the picture it looks like iron staining . Bit of moisture and the nails have rusted a little and stained the timber. I'd say probably unlikely to sand out although they may lighten a touch. Personally I wouldn't worry about filling the nail holes , never really looks right and the nails look so much more traditional . Still personal choice and if you want to go ahead . I'd use wudfil or car body filler and colour it to match the timber.
 
Following ladylola, who is usually right:

The staining is probably rust, perhaps due to wet mopping the floor or due to the joists being damp. If its a ground floor, is there good ventilation below the floor?
A long shot would be due to some kind of chemical reaction with the present sealer.

Before sanding all the nails must be driven below the surface or they will snag and rip the sanding paper.

Presuming that the boards are T&G you can only remove a few mm's - so be cautious if using a floor sanding machine.
 
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Personally I like the iron oxide staining. It shows it's original and not laid last week.
 
Knocking the nails further in is a must when doing this.
 
Def knock the nail heads down to just below the level you will sand to - as ree says above, you'll shred your sanding belts otherwise and that gets expensive...
If you do need to fill indentations or hairline cracks either side of the slivers, use one of the fillers where the dust from the final sand is mixed with the clear formulation. Bona make one called mixed-and-fill but there are other manufacturers. Benefit here is that the the cured product dries close to the tone of the wood you sourced the dust from.

You can also use this to fill over the recessed nail heads, though personally I agree with joe-90 above on his (subjective) suggestion to leave them visible!
 
I have yet to see a method of filling gaps in sanded floorboards that both works long term and looks any good. I would leave it well alone. A sanded Victorian floor is what it is.
 

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